#include <BALL/FORMAT/SDFile.h>

Inheritance diagram for BALL::SDFile:

Public Member Functions
Constructors and Destructors
	SDFile ()

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

virtual	~SDFile ()
	Destructor. More...

Reading and Writing of Kernel Datastructures
virtual bool	write (const System &system)

virtual bool	write (const Molecule &molecule)

virtual bool	read (System &system)

virtual Molecule *	read ()

void	disableAtoms ()

void	enableAtoms ()

const SDFile &	operator= (const SDFile &file)

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

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

virtual	~MOLFile ()
	Destructor. More...

const MOLFile &	operator= (const MOLFile &file)

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 ()

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

Protected Member Functions
void	readPropertyBlock_ (Molecule &molecule)

void	writePropertyBlock_ (const Molecule &molecule)

Protected Member Functions inherited from BALL::MOLFile
Molecule *	readCTAB_ (std::vector< Atom * > &atom_map)

bool	readCountsLine_ (CountsStruct &counts)
	Read the Counts line of a MOL file. More...

bool	readAtomLine_ (AtomStruct &atom)
	Read a line from the atom block. More...

bool	readBondLine_ (BondStruct &bond)
	Read a line from the bond block. More...

void	writeCountsLine_ (const CountsStruct &counts)
	Write the Counts line. More...

void	writeAtomLine_ (const AtomStruct &atom)
	Write a line of the atom block. More...

void	writeBondLine_ (const BondStruct &bond)
	Write a line of the bond block. More...

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

virtual void	initWrite_ ()

Protected Attributes
bool	read_atoms_

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
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)

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::MOLFile
static const String	counts_format_
	The format of the counts line. More...

static const String	atom_format_
	The format of an entry of the atom block. More...

static const String	bond_format_
	The format of an entry of the bond block. More...

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

static TransformationManager	transformation_manager_

static Size	transformation_methods_

Detailed Description

MDL SD file class. This class enables BALL to read and write MDL SD files.

: A description of this file format (and the related MOLFile format) can be obtained from the MDL webpage http://www.mdli.com

Definition at line 22 of file SDFile.h.

Constructor & Destructor Documentation

BALL::SDFile::SDFile ( )

Default constructor

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

Detailed constructor.

Exceptions

Exception::FileNotFound if the file could not be opened

virtual BALL::SDFile::~SDFile ( )

virtual

Destructor.

Member Function Documentation

void BALL::SDFile::disableAtoms ( )

Do not read atoms and bonds. This (seemingly strange) option allows the user to read the properties of the molecules only. Since SD files can contain all kinds of information besides the molecular structure and reading the structure can be rather time and space consuming, you can disable it with this option. The read and write methods will still create molecules, but they will be empty. However, the NamedProperties of the molecules contain the optional information contained in the SD file.

void BALL::SDFile::enableAtoms ( )

Read atoms and bonds.

See also: disableAtoms

const SDFile& BALL::SDFile::operator= ( const SDFile & file )

virtual bool BALL::SDFile::read ( System & system )

virtual

Read a system from the SD file

Exceptions

Exception::ParseError if a syntax error was encountered

Reimplemented from BALL::MOLFile.

virtual Molecule* BALL::SDFile::read ( )

virtual

Read a single molecule from an SD file.

Exceptions

Exception::ParseError if a syntax error was encountered

Reimplemented from BALL::MOLFile.

void BALL::SDFile::readPropertyBlock_ ( Molecule & molecule )

protected

Read the property block of an SD file. The values are stored as named properties in the molecule read.

virtual bool BALL::SDFile::write ( const System & system )

virtual

Write a system to the SD file. Write all molecules contained in the system to the SD file. All named properties are included in the property section.

Exceptions

File::CannotWrite if writing to the file failed

Reimplemented from BALL::MOLFile.

virtual bool BALL::SDFile::write ( const Molecule & molecule )

virtual

Append a single molecule to the SD file.

Exceptions

File::CannotWrite if writing to the file failed

Reimplemented from BALL::MOLFile.

void BALL::SDFile::writePropertyBlock_ ( const Molecule & molecule )

protected

Read the propertyblock of an SD file. The values are stored as named properties in the molecule read.

Member Data Documentation

bool BALL::SDFile::read_atoms_

protected

Whether atoms and bonds should be read

Definition at line 110 of file SDFile.h.

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation