#include <BALL/FORMAT/dockResultFile.h>

Inheritance diagram for BALL::DockResultFile:

Public Member Functions
	DockResultFile ()

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

virtual	~DockResultFile () throw ()

Receptor *	readReceptor () throw (Exception::ParseError)

void	writeReceptor (Receptor *s)

Ligand *	readLigand () throw (Exception::ParseError)

bool	writeLigand (Ligand *lig)

void	writeResult (Result *res)

void	writeResults (vector< Result * > &res)

vector< Result * >	readResults () throw (Exception::ParseError)

void	close ()

const vector< Result * > *	getResults ()

void	addResult (Result *res)

Size	countConformations ()

GenericMolecule interface functions
Molecule *	read () throw (Exception::ParseError)

bool	write (const Molecule &mol) throw (File::CannotWrite)

void	setOutputParameters (Result::Method, String property_name, String &receptor_conf_UID, String method_description="")

void	setToolInfo (const String &toolinfo, const String &timestamp)

void	setInputParameters (list< Size > &selected_results)

void	selectAllResultsForInput ()

void	disableAutomaticResultCreation ()

const FlexibleMolecule *	getCurrentLigand ()

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

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

virtual	~GenericMolFile ()

const GenericMolFile &	operator= (const GenericMolFile &rhs)

void	defineInputAsTemporary (bool b=true)

void	enableOutputCompression (String zipped_filename)

bool	isCompressedFile ()

virtual bool	write (const System &system)

virtual bool	read (System &system)

virtual GenericMolFile &	operator>> (System &system)

virtual GenericMolFile &	operator<< (const System &system)

virtual GenericMolFile &	operator>> (Molecule &molecule)

virtual GenericMolFile &	operator<< (const Molecule &molecule)

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)

void	clear ()

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

Static Public Attributes
static bool	SHOW_IDENTICAL_LIGANDS_WARNING

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...

Additional Inherited Members
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 }

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)

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

virtual void	initWrite_ ()

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_

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

static TransformationManager	transformation_manager_

static Size	transformation_methods_

Detailed Description

DockResultFile class. Used to store docking results.

Definition at line 27 of file dockResultFile.h.

Constructor & Destructor Documentation

BALL::DockResultFile::DockResultFile ( )

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

virtual BALL::DockResultFile::~DockResultFile	(	)
throw	(
	)

virtual

Member Function Documentation

void BALL::DockResultFile::addResult ( Result * res )

void BALL::DockResultFile::close ( )

virtual

Close file.

Reimplemented from BALL::GenericMolFile.

Size BALL::DockResultFile::countConformations ( )

Return the number of unique conformations currently stored in the result-sections of this DockResultFile.

void BALL::DockResultFile::disableAutomaticResultCreation ( )

Disables the automatic creation of Results-items when using write(const Molecule& mol). However, this is only necessary when merging/sorting DockingFiles when Results are set manually.

const FlexibleMolecule* BALL::DockResultFile::getCurrentLigand ( )

Return the current Ligand object that was created by the last call of read() or write(const Molecule& mol).

const vector<Result*>* BALL::DockResultFile::getResults ( )

Molecule* BALL::DockResultFile::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.

Ligand* BALL::DockResultFile::readLigand	(		)
throw	(	Exception::ParseError
	)

Read receptor object.

Returns: Ligand* pointer to the read Ligand object

Receptor* BALL::DockResultFile::readReceptor	(		)
throw	(	Exception::ParseError
	)

Read receptor object.

Returns: Receptor* pointer to the read Receptor object

vector<Result*> BALL::DockResultFile::readResults	(		)
throw	(	Exception::ParseError
	)

Read result objects.

Returns: vector of Result pointers

void BALL::DockResultFile::selectAllResultsForInput ( )

void BALL::DockResultFile::setInputParameters ( list< Size > & selected_results )

void BALL::DockResultFile::setOutputParameters	(	Result::Method	,
		String	property_name,
		String &	receptor_conf_UID,
		String	method_description = `""`
	)

void BALL::DockResultFile::setToolInfo	(	const String &	toolinfo,
		const String &	timestamp
	)

bool BALL::DockResultFile::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.

Exceptions

File::CannotWrite if writing to the file failed

Reimplemented from BALL::GenericMolFile.

bool BALL::DockResultFile::writeLigand ( Ligand * lig )

Write Ligand object (directly).

Parameters

pointer to Ligand object

void BALL::DockResultFile::writeReceptor ( Receptor * s )

Write receptor object (directly).

Parameters

pointer to Receptor object

void BALL::DockResultFile::writeResult ( Result * res )

Write Result object (directly).

Parameters

pointer to Result object

void BALL::DockResultFile::writeResults ( vector< Result * > & res )

Write vector of Result objects (directly).

Parameters

vector of pointers to Result objects

Member Data Documentation

bool BALL::DockResultFile::SHOW_IDENTICAL_LIGANDS_WARNING

static

Definition at line 31 of file dockResultFile.h.

Public Member Functions

Static Public Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation