#include <BALL/FORMAT/genericMolFile.h>

Inheritance diagram for BALL::GenericMolFile:

Public Member Functions
Constructors and Destructors
	GenericMolFile ()

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

virtual	~GenericMolFile ()

virtual void	close ()

Assignment
const GenericMolFile &	operator= (const GenericMolFile &rhs)

void	defineInputAsTemporary (bool b=true)

void	enableOutputCompression (String zipped_filename)

bool	isCompressedFile ()

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 ()

Operators
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
virtual void	initRead_ ()

virtual void	initWrite_ ()

Protected Attributes
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::File
static HashSet< String >	created_temp_filenames_

static TransformationManager	transformation_manager_

static Size	transformation_methods_

Detailed Description

Base class for all molecule file format classes. This class provides an interface for all molecular structure formats (except for PDB files, due to their complex and capricious structure and contents).

: GenericMolFile supports two type of operations: reading/writing single molecules and reading/writing systems (i.e. collections of molecules).

: When reading molecules, the structures are read one at a time from the file in the order they are stored. In contrast, reading systems retrieves all structures contained in the file. For file formats that do not support multiple structure in a file (e.g. the MDL MOLFile ), those two operations are basically equivalent. A fundamental difference however is the fact that reading a molecule create a new molecule, whereas reading a system adds the molecules read to an existing instance of System . This implies that the system has to be cleared prior to reading a system if that incremental behaviour is not desired.

: The user interface of the class is mainly provided through the stream operator. A typical example for reading a structure from a HyperChem file might look as follows:

: {verbatim} HINFile hinfile(filename); System S; hinfile >> S; {verbatim} This interface applies to all derived classes as well, so that file formats can be exchanged conveniently.

: GenericMolFile is derived from LineBasedFile since most molecular structure formats are line-based tagged formats, often containing Fortran-style formatted sections. LineBasedFile provides a number of convenient methods to parse that kind of format.

Definition at line 56 of file genericMolFile.h.

Constructor & Destructor Documentation

BALL::GenericMolFile::GenericMolFile ( )

Default constructor

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

Detailed constructor

Exceptions

Exception::FileNotFound if the file could not be opened

virtual BALL::GenericMolFile::~GenericMolFile ( )

virtual

Destructor

Member Function Documentation

virtual void BALL::GenericMolFile::close ( )

virtual

Reimplemented in BALL::DockResultFile.

void BALL::GenericMolFile::defineInputAsTemporary ( bool b = true )

Define the input file to be a temporary file (e.g. an unzipped file). In this case, the input file will be deleted when this GenericMolFile is closed.

void BALL::GenericMolFile::enableOutputCompression ( String zipped_filename )

Enable compression of the output file. If enabled, the output-file will be gzip'ed. Output will be stored under the specified filename and the original (uncompressed) output file will be deleted.

virtual void BALL::GenericMolFile::initRead_ ( )

protectedvirtual

Initialize internals for read. This method is called by the default implementation of read(System& system) . Its purpose is the initialization of internal members holding, for example, header information from the file. The default implementation provided is empty.

Reimplemented in BALL::GAMESSLogFile, BALL::GAMESSDatFile, and BALL::HINFile.

virtual void BALL::GenericMolFile::initWrite_ ( )

protectedvirtual

Initialize internals for write. Same functionality as initRead , but is called prior to writing a system.

bool BALL::GenericMolFile::isCompressedFile ( )

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

virtual

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

Exceptions

File::CannotWrite if writing to the file failed

Reimplemented in BALL::PDBFile.

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

virtual

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

Exceptions

File::CannotWrite if writing to the file failed

Reimplemented in BALL::PDBFile.

const GenericMolFile& BALL::GenericMolFile::operator= ( const GenericMolFile & rhs )

Assignment operator. Create a new object pointing to the same filename.

Exceptions

Exception::FileNotFound if the file could not be opened

virtual GenericMolFile& BALL::GenericMolFile::operator>> ( System & system )

virtual

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

Exceptions

Exception::ParseError if a syntax error was encountered

Reimplemented in BALL::PDBFile.

virtual GenericMolFile& BALL::GenericMolFile::operator>> ( Molecule & molecule )

virtual

Stream operator for reading a molecule. Calls read()

Exceptions

Exception::ParseError if a syntax error was encountered

Reimplemented in BALL::PDBFile.

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

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 in BALL::PDBFile, BALL::MOLFile, BALL::GAMESSDatFile, BALL::GAMESSLogFile, BALL::MOL2File, BALL::HINFile, BALL::KCFFile, BALL::XYZFile, BALL::MOPACOutputFile, BALL::SDFile, and BALL::AntechamberFile.

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

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 in BALL::PDBFile, BALL::MOLFile, BALL::GAMESSDatFile, BALL::GAMESSLogFile, BALL::MOL2File, BALL::KCFFile, BALL::DockResultFile, BALL::XYZFile, BALL::HINFile, BALL::MOPACOutputFile, BALL::SDFile, and BALL::AntechamberFile.

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

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.

Exceptions

File::CannotWrite if writing to the file failed

Reimplemented in BALL::PDBFile, BALL::MOLFile, BALL::GAMESSDatFile, BALL::GAMESSLogFile, BALL::MOL2File, BALL::MOPACInputFile, BALL::KCFFile, BALL::HINFile, BALL::XYZFile, BALL::AntechamberFile, and BALL::SDFile.

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

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 in BALL::PDBFile, BALL::MOLFile, BALL::MOL2File, BALL::DockResultFile, BALL::GAMESSDatFile, BALL::GAMESSLogFile, BALL::XYZFile, BALL::AntechamberFile, BALL::KCFFile, BALL::HINFile, BALL::MOPACInputFile, and BALL::SDFile.

Member Data Documentation

bool BALL::GenericMolFile::compress_output_

protected

Definition at line 195 of file genericMolFile.h.

bool BALL::GenericMolFile::gmf_is_closed_

protected

Definition at line 196 of file genericMolFile.h.

bool BALL::GenericMolFile::input_is_temporary_

protected

Definition at line 194 of file genericMolFile.h.

String BALL::GenericMolFile::zipped_filename_

protected

Definition at line 197 of file genericMolFile.h.

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation