#include <BALL/FORMAT/XYZFile.h>

Inheritance diagram for BALL::XYZFile:

Public Member Functions
Constructors and Destructors
	XYZFile ()

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

virtual	~XYZFile ()

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

Reading and Writing of Kernel Datastructures
virtual bool	write (const AtomContainer &ac)

virtual bool	write (const System &system)

virtual bool	write (const Molecule &mol)

virtual bool	read (System &system)

virtual Molecule *	read ()

BALL_DEPRECATED const String &	getComent () const

const String &	getComment () const

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...

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

XYZ file class. This class enables BALL to read and write XMol XYZ files. The XYZ format is a very simple molecular file format. In general it contains only the atom type (i.e., the element) and the cartesian coordinates of the structure. Newer versions of this file format also contain bonds (without bond order) and atom names.

: The first line of each XYZ file contains a single integer number: the number of atoms in the file. The second line is just a comment line. When reading a XYZ file, BALL stores this comment as the name attribute of the system read. Similarly, on writing the system, it's name is written to this comment line. All remaining lines contain the element symbol and the three coordinates in free format.

Definition at line 34 of file XYZFile.h.

Constructor & Destructor Documentation

BALL::XYZFile::XYZFile ( )

Default constructor

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

Detailed constructor. Create a XYZ file and open it with mode open_mode (reading is default)

Parameters

filename	the filename
open_mode	the openmode - default is File::IN

Exceptions

Exception::FileNotFound if the file could not be opened

virtual BALL::XYZFile::~XYZFile ( )

virtual

Destructor

Member Function Documentation

BALL_DEPRECATED const String& BALL::XYZFile::getComent ( ) const

inline

Deprecated:: Instead of this method use XYZFile::getComment()

Definition at line 90 of file XYZFile.h.

const String& BALL::XYZFile::getComment ( ) const

inline

Definition at line 93 of file XYZFile.h.

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

virtual

Read a system from the XYZ file

Exceptions

Exception::ParseError if a syntax error was encountered

Reimplemented from BALL::GenericMolFile.

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

virtual

Read a molecule from the XYZ file

Exceptions

Exception::ParseError if a syntax error was encountered

Reimplemented from BALL::GenericMolFile.

virtual bool BALL::XYZFile::write ( const AtomContainer & ac )

virtual

Write an AtomContainer to the XYZ file

Exceptions

File::CannotWrite if writing to the file failed

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

virtual

Write a system to the XYZ file

Exceptions

File::CannotWrite if writing to the file failed

Reimplemented from BALL::GenericMolFile.

virtual bool BALL::XYZFile::write ( const Molecule & mol )

virtual

Write a molecule to the XYZ file

Exceptions

File::CannotWrite if writing to the file failed

Reimplemented from BALL::GenericMolFile.

Public Member Functions

Reading and Writing of Kernel Datastructures

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation