#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 Types inherited from BALL::File
typedef std::ios::openmode	OpenMode

enum	Transformation { TRANSFORMATION__EXEC = 1, TRANSFORMATION__FILTER = 2, TRANSFORMATION__URL = 3 }

enum	Type { TYPE__UNKNOWN = 0, TYPE__DIRECTORY = 1, TYPE__CHAR_SPECIAL_FILE = 2, TYPE__BLOCK_SPECIAL_FILE = 3, TYPE__REGULAR_FILE = 4, TYPE__SYMBOLIC_LINK = 5, TYPE__SOCKET = 6, TYPE__FIFO_SPECIAL_FILE = 7 }

Public Member Functions
virtual bool	hasFormat ()
	Check whether the current file is in PDB format. More...

Constructurs and destructor.
	PDBFile ()

	PDBFile (const String &filename, File::OpenMode open_mode=std::ios::in)

	PDBFile (const Options &new_options)

virtual	~PDBFile ()

Assignment.
virtual void	clear (int state)
	Clear the stream state. More...

virtual void	clear ()
	Clear all members. More...

Accessors.
virtual float	getVersion () const
	Returns the version number this PDB file reader is able to read. More...

void	open (const String &name, File::OpenMode open_mode=std::ios::in)

void	selectModel (Index index)

void	selectAltLocationIndicator (char c)

Index	getSelectedModel () const
	Return the model currently selected. More...

void	selectAllModels ()
	Selects all models for reading. More...

Index	getCurrentModel () const
	Returns the number of the model weare currently reading. (?????) More...

char *	getRecordString ()
	Return a mutable pointer to the line buffer. More...

const char *	getRecordString () const
	Return a constant pointer to the line buffer. More...

Index	getRecordNumber () const
	Returns the number of the record we are currently reading. More...

PDB::RecordType	getRecordType () const
	Returns the type of the record we are currently reading. More...

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. More...

virtual char	getAtomRemotenessIndicator (const PDB::Atom atom_name)
	Extract the PDB remoteness indicator of an atom record. More...

virtual short	getAtomBranchDesignator (const PDB::Atom atom_name)
	Extract the PDB branch designator of an atom record. More...

Size	countRecordFields () const
	Returns the number of record fields. More...

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(). More...

bool	readLine (char *line, Size size, bool extract_values)
	Read and parse a line from a PDB file. More...

bool	readFirstRecord (bool read_values=true)
	Read the firts record of a file. More...

bool	readNextRecord (bool read_values=true)
	Read the next record of a PDB file. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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)

PDBFile &	operator>> (Molecule &molecule)

PDBFile &	operator>> (System &system)

PDBFile &	operator<< (const Protein &protein)

PDBFile &	operator<< (const System &system)

PDBFile &	operator<< (const Molecule &molecule)

bool	read (Protein &protein)

bool	read (Molecule &protein)

bool	read (System &system)

Molecule *	read ()

bool	write (const Protein &protein)

bool	write (const Molecule &molecule)

bool	write (const System &system)

bool	write (const System &system, const PDBInfo &info)

Public Member Functions inherited from BALL::GenericMolFile
	GenericMolFile ()

	GenericMolFile (const String &filename, File::OpenMode open_mode=std::ios::in)

virtual	~GenericMolFile ()

virtual void	close ()

const GenericMolFile &	operator= (const GenericMolFile &rhs)

void	defineInputAsTemporary (bool b=true)

void	enableOutputCompression (String zipped_filename)

bool	isCompressedFile ()

Public Member Functions inherited from BALL::LineBasedFile
	LineBasedFile ()
	Default constructor. More...

	LineBasedFile (const String &filename, File::OpenMode open_mode=std::ios::in, bool trim_whitespaces=false)

bool	operator== (const LineBasedFile &f)

bool	operator!= (const LineBasedFile &f)

const LineBasedFile &	operator= (const LineBasedFile &file)

Position	getLineNumber () const
	Get the last line number in the file. More...

const String &	getLine () const
	Return the current line. More...

String &	getLine ()
	Return the current line. More...

bool	readLine ()

bool	skipLines (Size number=1)

bool	search (const String &text, bool return_to_start=false)

bool	search (const String &text, const String &stop, bool return_to_start=false)

bool	gotoLine (Position line_number)

void	rewind ()

void	test (const char *file, int line, bool condition, const String &msg) const

String	getField (Index pos=0, const String &quotes="", const String &delimiters=String::CHARACTER_CLASS__WHITESPACE) const

bool	startsWith (const String &text) const
	Test if the current line starts with text. More...

bool	has (const String &text) const
	Return true if the current line contains text. More...

Index	switchString (const std::vector< String > &data) const

bool	parseColumnFormat (const char format, Position index, Size length, void arg)

void	enableTrimWhitespaces (bool state)
	Set wheter leading and trailing whitespaces in lines shall be removed. More...

bool	trimWhiteSpacesEnabled () const

Public Member Functions inherited from BALL::File
	File ()

	File (const String &name, OpenMode open_mode=std::ios::in)

virtual	~File ()

bool	isValid () const

bool	open (const String &name, File::OpenMode open_mode=std::ios::in)

bool	reopen ()

bool	reopen (File::OpenMode open_mode)

void	close ()

const String &	getName () const

void	setName (const String &name)

const String &	getOriginalName () const

Size	getSize ()

File::OpenMode	getOpenMode () const

Type	getType (bool trace_link) const

bool	copyTo (const String &destination_name, Size buffer_size=4096)

bool	moveTo (const String &destination_name)

bool	remove ()

bool	renameTo (const String &new_path)

bool	truncate (Size size=0)

std::fstream &	getFileStream ()

TransformationManager &	getTransformationManager ()

const TransformationManager &	getTransformationManager () const

bool	operator== (const File &file) const

bool	operator!= (const File &file) const

bool	isOpen () const

bool	isClosed () const

bool	isAccessible () const

bool	isCanonized () const

bool	isReadable () const

bool	isWritable () const

bool	isExecutable () const

Public Member Functions inherited from BALL::PropertyManager
BALL_INLINE	PropertyManager ()
	Default constructor. More...

BALL_INLINE	PropertyManager (const PropertyManager &property_manager)
	Copy constructor. More...

virtual	~PropertyManager ()
	Destructor. More...

virtual void	destroy ()
	Clears all properties. More...

void	set (const PropertyManager &property_manager)

const PropertyManager &	operator= (const PropertyManager &property_manager)

void	get (PropertyManager &property_manager) const

void	swap (PropertyManager &property_manager)

BitVector &	getBitVector ()

const BitVector &	getBitVector () const

	operator BitVector & ()

void	setProperty (Property property)

void	clearProperty (Property property)

void	toggleProperty (Property property)

Size	countProperties () const

const NamedProperty &	getNamedProperty (Position index) const

NamedProperty &	getNamedProperty (Position index)

void	setProperty (const NamedProperty &property)

void	setProperty (const std::string &name)

void	setProperty (const std::string &name, bool value)

void	setProperty (const std::string &name, int value)

void	setProperty (const std::string &name, unsigned int value)

void	setProperty (const std::string &name, float value)

void	setProperty (const std::string &name, double value)

void	setProperty (const std::string &name, const std::string &value)

void	setProperty (const std::string &name, const PersistentObject &value)

const NamedProperty &	getProperty (const std::string &name) const

NamedPropertyIterator	beginNamedProperty ()

NamedPropertyIterator	endNamedProperty ()

void	clearProperty (const std::string &name)

Size	countNamedProperties () const

bool	hasProperty (Property property) const
	Query for an unnamed property. More...

bool	hasProperty (const std::string &name) const
	Query for a named property. More...

bool	operator== (const PropertyManager &pm) const

bool	operator!= (const PropertyManager &pm) const
	Inequality operator. More...

void	write (PersistenceManager &pm) const
	Persistent stream writing. More...

bool	read (PersistenceManager &pm)
	Persistent stream reading. More...

bool	isValid () const

void	dump (std::ostream &s=std::cout, Size depth=0) const

Public Attributes
Options
Options	options
	The options for parsing the file. More...

PDBInfo	info
	Summary information on the last file read. More...

Protected Member Functions
	PDBFile (const File &pdbf)

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. More...

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)

Protected Member Functions inherited from BALL::GenericMolFile
virtual void	initRead_ ()

virtual void	initWrite_ ()

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. More...

int	verbosity_
	_Verbosity level More...

bool	strict_line_checking_

Index	selected_model_
	The selected model_. More...

bool	store_skipped_records_
	Store the skipped records in info? More...

bool	ignore_xplor_pseudo_atoms_
	Ignore XPLOR pseudo atoms? More...

bool	parse_partial_charges_
	Read partial charges from cols 76-80? More...

bool	write_pdbformat_1996_
	write in the 1996-format? More...

bool	read_done_

Protected Attributes inherited from BALL::GenericMolFile
bool	input_is_temporary_

bool	compress_output_

bool	gmf_is_closed_

String	zipped_filename_

Protected Attributes inherited from BALL::LineBasedFile
String	line_
	buffer for the line in use More...

Position	line_number_
	line number in the file More...

bool	trim_whitespaces_

vector< char >	col_buffer_
	buffer for column parsing More...

Protected Attributes inherited from BALL::File
String	name_

String	original_name_

OpenMode	open_mode_

bool	is_open_

bool	is_temporary_

Additional Inherited Members
Static Public Member Functions inherited from BALL::File
static Size	getSize (String name)

static Type	getType (String name, bool trace_link)

static bool	copy (String source_name, String destination_name, Size buffer_size=4096)

static bool	move (const String &source_name, const String &destination_name)

static bool	remove (String name)

static bool	rename (String old_path, String new_path)

static bool	truncate (String path, Size size=0)

static bool	createTemporaryFilename (String &temporary, const String &suffix=".TMP")

static void	enableTransformation (Transformation transformation)

static void	disableTransformation (Transformation transformation)

static bool	isTransformationEnabled (Transformation transformation)

static void	registerTransformation (const String &pattern, const String &exec)

static void	unregisterTransformation (const String &pattern)

static bool	isAccessible (String name)

static bool	isReadable (String name)

static bool	isWritable (String name)

static bool	isExecutable (String name)

Static Public Attributes inherited from BALL::File
static const OpenMode	MODE_IN
	Open for input (default) More...

static const OpenMode	MODE_OUT
	Open for output. More...

static const OpenMode	MODE_APP
	Append. Seek to end before each write operation. More...

static const OpenMode	MODE_BINARY
	Binary mode. More...

static const OpenMode	MODE_ATE
	Seek to end directly after opening. More...

static const OpenMode	MODE_TRUNC
	Truncate an existing file. More...

static const String	TRANSFORMATION_EXEC_PREFIX
	Prefix for filenames that are created through the execution of commands "exec:". More...

static const String	TRANSFORMATION_FILE_PREFIX
	Prefix for files (to mimick URL-like behavior) "file:". More...

static const String	TRANSFORMATION_FTP_PREFIX
	Prefix for FTP-transfers "ftp://". More...

static const String	TRANSFORMATION_HTTP_PREFIX
	Prefix for HTTP-transfer "http://". More...

Static Protected Attributes inherited from BALL::File
static HashSet< String >	created_temp_filenames_

static TransformationManager	transformation_manager_

static Size	transformation_methods_

Detailed Description

PDB file class.

Definition at line 55 of file PDBFile.h.

Member Typedef Documentation

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

Definition at line 634 of file PDBFile.h.

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

Definition at line 637 of file PDBFile.h.

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

Definition at line 636 of file PDBFile.h.

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

Definition at line 635 of file PDBFile.h.

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

Definition at line 638 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`
	)

File-like constructor

Exceptions

Exception::FileNotFound if the file could not be opened

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

Construct with options.

virtual BALL::PDBFile::~PDBFile ( )

virtual

Destructor

BALL::PDBFile::PDBFile ( const File & pdbf )

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 ( int state )

virtual

Clear the stream state.

virtual void BALL::PDBFile::clear ( )

virtual

Clear all members.

Reimplemented from BALL::PropertyManager.

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
	)

staticprotected

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::RecordANISOU &	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::RecordAUTHOR &	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::RecordCISPEP &	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::RecordCONECT &	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::RecordDBREF &	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::RecordENDMDL &	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::RecordFORMUL &	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::RecordHEADER &	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::RecordHET &	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::RecordHETNAM &	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::RecordHYDBND &	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::RecordKEYWDS &	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::RecordMASTER &	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::RecordMODRES &	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::RecordMTRIX2 &	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::RecordOBSLTE &	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::RecordORIGX2 &	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::RecordREMARK &	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::RecordSCALE1 &	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::RecordSCALE3 &	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::RecordSEQRES &	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::RecordSIGATM &	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::RecordSITE &	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::RecordSOURCE &	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::RecordSSBOND &	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::RecordTITLE &	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::RecordTVECT &	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.

char* BALL::PDBFile::getRecordString ( )

Return a mutable pointer to the line buffer.

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

Return a constant 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::RecordANISOU & record )

virtual

Reads an anisotropic temperature factor record.

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

virtual

Reads an atom record.

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

virtual

Reads an author record.

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

virtual

Reads a caveat record.

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::RecordCOMPND & record )

virtual

Reads the title record containing macroscopic compoubd information.

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

virtual

Reads a connection record.

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::RecordDBREF & record )

virtual

Reads a record containing database cross-reference links.

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::RecordENDMDL & record )

virtual

Reads a model ending record.

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::RecordFORMUL & record )

virtual

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

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

virtual

Reads a record containing a footnote.

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::RecordHELIX & record )

virtual

Reads a helix defining record.

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::RecordHETATM & record )

virtual

Reads atomic coordinates for atoms in non-standard groups.

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::RecordHETSYN & record )

virtual

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

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

virtual

Reads a record defining a hydrogen bond.

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

virtual

Reads a record containing a journal reference.

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::RecordLINK & record )

virtual

Reads a record containing supplemental connectivity information.

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::RecordMODEL & record )

virtual

Reads a record indicating the beginning of a new model.

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

virtual

Reads a record identifying residue modifications.

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::RecordMTRIX2 & record )

virtual

Reads a record defining transformations expressing non-crystallographic symmetry.

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::RecordOBSLTE & record )

virtual

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

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::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::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::RecordREMARK & record )

virtual

Reads a record containing remarks.

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

virtual

Reads a record containing a revision history.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordSCALE1 & 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::RecordSCALE3 & record )

virtual

Reads a scale transformation record.

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::RecordSEQRES & record )

virtual

Reads a record containing the sequence of residues.

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

virtual

Reads a record defining a beta-sheet.

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::RecordSIGUIJ & record )

virtual

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

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::RecordSLTBRG & record )

virtual

Reads a record defining a salt bridge.

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::RecordSPRSDE & record )

virtual

List of entries this file supersedes.

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

virtual

Reads a record specifying a disulfide bond.

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

virtual

Reads a record terminating molecule.

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::RecordTURN & record )

virtual

Reads a record specifying a turn.

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

virtual

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

static bool BALL::PDBFile::isHeteroAtom_ ( const Atom & atom )

staticprotected

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.

void BALL::PDBFile::open	(	const String &	name,
		File::OpenMode	open_mode = `std::ios::in`
	)

PDBFile& BALL::PDBFile::operator<< ( const Protein & protein )

Write a protein to the file

Exceptions

File::CannotWrite if writing to the file failed

PDBFile& BALL::PDBFile::operator<< ( const System & system )

virtual

Write a system to the file

Exceptions

File::CannotWrite if writing to the file failed

Reimplemented from BALL::GenericMolFile.

PDBFile& BALL::PDBFile::operator<< ( const Molecule & molecule )

virtual

Write molecule to the file

Exceptions

File::CannotWrite if writing to the file failed

Reimplemented from BALL::GenericMolFile.

PDBFile& BALL::PDBFile::operator= ( const PDBFile & pdbf )

protected

PDBFile& BALL::PDBFile::operator>> ( Protein & protein )

Read a protein from the file

Exceptions

Exception::ParseError if a syntax error was encountered

PDBFile& BALL::PDBFile::operator>> ( Molecule & molecule )

virtual

Read a molecule from the file

Exceptions

Exception::ParseError if a syntax error was encountered

Reimplemented from BALL::GenericMolFile.

PDBFile& BALL::PDBFile::operator>> ( System & system )

virtual

Read system from the file

Exceptions

Exception::ParseError if a syntax error was encountered

Reimplemented from BALL::GenericMolFile.

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

bool BALL::PDBFile::read ( Protein & protein )

Read a Protein from the file return true if the Protein was read successfully return false otherwise

Exceptions

Exception::ParseError if a syntax error was encountered

bool BALL::PDBFile::read ( Molecule & protein )

Read a Molecule from the file return true if the Molecule was read successfully return false otherwise

Exceptions

Exception::ParseError if a syntax error was encountered

bool BALL::PDBFile::read ( System & system )

virtual

Read a System from the file return true if the System was read successfully return false otherwise

Exceptions

Exception::ParseError if a syntax error was encountered

Reimplemented from BALL::GenericMolFile.

Molecule* BALL::PDBFile::read ( )

virtual

Read a Molecule from the file

Returns: Molecule* pointer to the newly created Molecule. 0 if no molecule could be read or if no further Molecule could be read.

Exceptions

Exception::ParseError if a syntax error was encountered

Reimplemented from BALL::GenericMolFile.

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
	)

staticprotected

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 Protein & protein )

Write a Protein to the file return true if the writing finished successfully return false otherwise

Exceptions

File::CannotWrite if writing to the file failed

bool BALL::PDBFile::write ( const Molecule & molecule )

virtual

Write a Molecule to the file return true if the writing finished successfully return false otherwise

Exceptions

File::CannotWrite if writing to the file failed

Reimplemented from BALL::GenericMolFile.

bool BALL::PDBFile::write ( const System & system )

virtual

Write a System to the file return true if the writing finished successfully return false otherwise

Exceptions

File::CannotWrite if writing to the file failed

Reimplemented from BALL::GenericMolFile.

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

Write a System to the file return true if the writing finished successfully return false otherwise

Exceptions

File::CannotWrite if writing to the file failed

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_	(	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.

See also: PDB::RecordType

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

protected

Write a SEQRES 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::RecordSHEET & helix )

protected

Write a SHEET 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::RecordSSBOND & helix )

protected

Write a SSBOND 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::RecordCRYST1 & cryst1 )

protected

Write a CRYST1 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::RecordMTRIX2 & mtrix2 )

protected

Write a MTRIX2 record to the current stream

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

protected

Write a MTRIX3 record to the current stream

void BALL::PDBFile::writeSecondaryStructureSection_	(	const PDB::Structure &	structure,
		const PDBInfo &	info
	)

protected

void BALL::PDBFile::writeSEQRESSection_ ( const std::vector< std::pair< char, String > > & chain_residues )

protected

void BALL::PDBFile::writeSHEETSection_ ( const PDB::Structure & structure )

protected

void BALL::PDBFile::writeSLTBRGSection_ ( const PDB::Structure & structure )

protected

void BALL::PDBFile::writeSSBONDSection_ ( const PDB::Structure & structure )

protected

void BALL::PDBFile::writeTitleSection_	(	const PDB::Structure &	structure,
		const PDBInfo &	info
	)

protected

void BALL::PDBFile::writeTURNSection_ ( const PDB::Structure & structure )

protected

Member Data Documentation

char BALL::PDBFile::alternate_location_indicator_

protected

Definition at line 858 of file PDBFile.h.

HashMap<const Atom*, Position> BALL::PDBFile::atom_map_

protected

Definition at line 872 of file PDBFile.h.

PDB::BookKeeping BALL::PDBFile::book_keeping_

protected

Book keeping struct for the number of records written.

Definition at line 875 of file PDBFile.h.

PDB::Character BALL::PDBFile::chain_ID_

protected

Definition at line 860 of file PDBFile.h.

PDB::AChar BALL::PDBFile::code_

protected

Definition at line 862 of file PDBFile.h.

PDB::RecordTypeFormat BALL::PDBFile::compare_record_type_format_

protected

Definition at line 845 of file PDBFile.h.

Chain* BALL::PDBFile::current_chain_

protected

Definition at line 865 of file PDBFile.h.

const Atom* BALL::PDBFile::current_const_atom_

protected

Definition at line 870 of file PDBFile.h.

const Chain* BALL::PDBFile::current_const_chain_

protected

Definition at line 866 of file PDBFile.h.

const Protein* BALL::PDBFile::current_const_protein_

protected

Definition at line 864 of file PDBFile.h.

const Residue* BALL::PDBFile::current_const_residue_

protected

Definition at line 868 of file PDBFile.h.

Index BALL::PDBFile::current_model_

protected

Definition at line 841 of file PDBFile.h.

PDBAtom* BALL::PDBFile::current_PDB_atom_

protected

Definition at line 869 of file PDBFile.h.

Protein* BALL::PDBFile::current_protein_

protected

Definition at line 863 of file PDBFile.h.

Index BALL::PDBFile::current_record_

protected

Definition at line 842 of file PDBFile.h.

PDB::RecordType BALL::PDBFile::current_record_type_

protected

Definition at line 844 of file PDBFile.h.

Residue* BALL::PDBFile::current_residue_

protected

Definition at line 867 of file PDBFile.h.

QuadrupleList BALL::PDBFile::helix_list_

protected

Definition at line 850 of file PDBFile.h.

bool BALL::PDBFile::ignore_xplor_pseudo_atoms_

protected

Ignore XPLOR pseudo atoms?

Definition at line 889 of file PDBFile.h.

PDBInfo BALL::PDBFile::info

Summary information on the last file read.

Definition at line 172 of file PDBFile.h.

PDB::AChar BALL::PDBFile::insertion_code_

protected

Definition at line 859 of file PDBFile.h.

char BALL::PDBFile::line_buffer_[PDB::SIZE_OF_PDB_LINE_BUFFER]

protected

Definition at line 837 of file PDBFile.h.

String BALL::PDBFile::name_

protected

Definition at line 871 of file PDBFile.h.

SecStructList BALL::PDBFile::new_helix_secstruc_list_

protected

Definition at line 854 of file PDBFile.h.

SecStructList BALL::PDBFile::new_sheet_secstruc_list_

protected

Definition at line 855 of file PDBFile.h.

SecStructList BALL::PDBFile::new_turn_secstruc_list_

protected

Definition at line 856 of file PDBFile.h.

Options BALL::PDBFile::options

The options for parsing the file.

Definition at line 170 of file PDBFile.h.

bool BALL::PDBFile::parse_partial_charges_

protected

Read partial charges from cols 76-80?

Definition at line 892 of file PDBFile.h.

PDBAtomMap BALL::PDBFile::PDB_atom_map_

protected

Definition at line 847 of file PDBFile.h.

bool BALL::PDBFile::read_done_

protected

Has the Protein already been read by use of read() ? If yes, the next call of read() will return 0. This is necesassry, since else the use of the GenericMolFile interface-function read() can result in endless loops.

Definition at line 899 of file PDBFile.h.

Size BALL::PDBFile::record_fields_

protected

Definition at line 843 of file PDBFile.h.

ResidueMap BALL::PDBFile::residue_map_

protected

Definition at line 848 of file PDBFile.h.

String BALL::PDBFile::residue_name_

protected

Definition at line 839 of file PDBFile.h.

Index BALL::PDBFile::residue_sequence_number_

protected

Definition at line 840 of file PDBFile.h.

Index BALL::PDBFile::selected_model_

protected

The selected model_.

Definition at line 883 of file PDBFile.h.

PDB::Integer BALL::PDBFile::sequence_number_

protected

Definition at line 861 of file PDBFile.h.

QuadrupleList BALL::PDBFile::sheet_list_

protected

Definition at line 851 of file PDBFile.h.

QuadrupleList BALL::PDBFile::ssbond_list_

protected

Definition at line 849 of file PDBFile.h.

bool BALL::PDBFile::store_skipped_records_

protected

Store the skipped records in info?

Definition at line 886 of file PDBFile.h.

bool BALL::PDBFile::strict_line_checking_

protected

Definition at line 880 of file PDBFile.h.

QuadrupleList BALL::PDBFile::turn_list_

protected

Definition at line 852 of file PDBFile.h.

int BALL::PDBFile::verbosity_

protected

_Verbosity level

Definition at line 878 of file PDBFile.h.

bool BALL::PDBFile::write_pdbformat_1996_

protected

write in the 1996-format?

Definition at line 895 of file PDBFile.h.

Classes

Public Types

Public Member Functions

Public Attributes

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation