#include <BALL/FORMAT/CIFFile.h>

Inheritance diagram for BALL::CIFFile:

Classes
class	Item
class	SaveFrame
class	Datacontent
class	Datablock
struct	State

Public Member Functions
Constructors and Destructors
	CIFFile ()
	CIFFile (const String &filename, File::OpenMode open_mode=std::ios::in)
virtual	~CIFFile ()
Reading and Writing of Crytallographic Information
virtual bool	write ()
virtual bool	read ()
Public Member Functions inherited from BALL::File
	File ()
	File (const String &name, OpenMode open_mode=std::ios::in)
virtual	~File ()
virtual void	clear ()
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

Accessors
static State	state
Molecule *	molecule_
String	current_datablock_
String	current_saveframe_
String	current_item_
StringHashMap< Index >	datablocks_hash_
vector< Datablock >	datablocks_
void	inSafeframe (const char *name)
void	inItem (const char *name)
void	inDatablock (const char *name)
void	insertDatablock (const Datablock &datablock)
const Datablock &	getDatablock (const String &name) const
Datablock &	getDatablock (const String &name)
bool	hasDatablock (const String &name) const
void	setMolecule (Molecule *molecule)
void	clearParameters ()
virtual void	initRead_ ()

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 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).
static const OpenMode	MODE_OUT
	Open for output.
static const OpenMode	MODE_APP
	Append. Seek to end before each write operation.
static const OpenMode	MODE_BINARY
	Binary mode.
static const OpenMode	MODE_ATE
	Seek to end directly after opening.
static const OpenMode	MODE_TRUNC
	Truncate an existing file.
static const String	TRANSFORMATION_EXEC_PREFIX
	Prefix for filenames that are created through the execution of commands "exec:".
static const String	TRANSFORMATION_FILE_PREFIX
	Prefix for files (to mimick URL-like behavior) "file:".
static const String	TRANSFORMATION_FTP_PREFIX
	Prefix for FTP-transfers "ftp://".
static const String	TRANSFORMATION_HTTP_PREFIX
	Prefix for HTTP-transfer "http://".
String	name_
String	original_name_
OpenMode	open_mode_
bool	is_open_
bool	is_temporary_
static HashSet< String >	created_temp_filenames_
static TransformationManager	transformation_manager_
static Size	transformation_methods_

Detailed Description

CIF file class. This class enables BALL to read and write input and output CIF files for the NMR shift application.

Definition at line 32 of file CIFFile.h.

Constructor & Destructor Documentation

◆ CIFFile() [1/2]

BALL::CIFFile::CIFFile ( )

Default constructor

◆ CIFFile() [2/2]

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

Detailed constructor

Exceptions

Exception::FileNotFound if the file could not be opened

◆ ~CIFFile()

virtual BALL::CIFFile::~CIFFile ( )

virtual

Destructor

Member Function Documentation

◆ clearParameters()

void BALL::CIFFile::clearParameters ( )

◆ getDatablock() [1/2]

Datablock & BALL::CIFFile::getDatablock ( const String & name )

◆ getDatablock() [2/2]

const Datablock & BALL::CIFFile::getDatablock ( const String & name ) const

◆ hasDatablock()

bool BALL::CIFFile::hasDatablock ( const String & name ) const

◆ inDatablock()

void BALL::CIFFile::inDatablock ( const char * name )

◆ inItem()

void BALL::CIFFile::inItem ( const char * name )

◆ initRead_()

virtual void BALL::CIFFile::initRead_ ( )

protectedvirtual

◆ inSafeframe()

void BALL::CIFFile::inSafeframe ( const char * name )

◆ insertDatablock()

void BALL::CIFFile::insertDatablock ( const Datablock & datablock )

◆ read()

virtual bool BALL::CIFFile::read ( )

virtual

Read a CIFFile.

Exceptions

Exception::ParseError if a syntax error was encountered

Reimplemented in BALL::NMRStarFile.

◆ setMolecule()

void BALL::CIFFile::setMolecule ( Molecule * molecule )

◆ write()

virtual bool BALL::CIFFile::write ( )

virtual

Write a CIFFile.

Exceptions

File::CannotWrite if writing to the file failed

Member Data Documentation

◆ current_datablock_

String BALL::CIFFile::current_datablock_

protected

Definition at line 276 of file CIFFile.h.

◆ current_item_

String BALL::CIFFile::current_item_

protected

Definition at line 278 of file CIFFile.h.

◆ current_saveframe_

String BALL::CIFFile::current_saveframe_

protected

Definition at line 277 of file CIFFile.h.

◆ datablocks_

vector<Datablock> BALL::CIFFile::datablocks_

protected

Definition at line 281 of file CIFFile.h.

◆ datablocks_hash_

StringHashMap<Index> BALL::CIFFile::datablocks_hash_

protected

Definition at line 280 of file CIFFile.h.

◆ molecule_

Molecule* BALL::CIFFile::molecule_

protected

Definition at line 274 of file CIFFile.h.

◆ state

State BALL::CIFFile::state

static

Definition at line 269 of file CIFFile.h.

Classes

Public Member Functions

Accessors

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CIFFile() [1/2]

◆ CIFFile() [2/2]

◆ ~CIFFile()

Member Function Documentation

◆ clearParameters()

◆ getDatablock() [1/2]

◆ getDatablock() [2/2]

◆ hasDatablock()

◆ inDatablock()

◆ inItem()

◆ initRead_()

◆ inSafeframe()

◆ insertDatablock()

◆ read()

◆ setMolecule()

◆ write()

Member Data Documentation

◆ current_datablock_

◆ current_item_

◆ current_saveframe_

◆ datablocks_

◆ datablocks_hash_

◆ molecule_

◆ state