#include <BALL/FORMAT/DCDFile.h>

Inheritance diagram for BALL::DCDFile:

Public Member Functions
Constructors and Destructor
	DCDFile ()
	Default constructor. More...

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

virtual	~DCDFile ()
	Destructor. More...

Assignment
virtual void	clear ()
	Clear method. More...

Predicates
bool	operator== (const DCDFile &file) const
	Equality operator. More...

bool	isSwappingBytes () const

bool	hasVelocities () const

Public methods for file handling
virtual bool	open (const String &name, File::OpenMode open_mode=std::ios::in)

bool	init ()

virtual bool	readHeader ()

virtual bool	writeHeader ()

virtual bool	seekAndWriteHeader ()

virtual bool	append (const SnapShot &snapshot)

virtual bool	read (SnapShot &snapshot)

virtual bool	flushToDisk (const std::vector< SnapShot > &buffer)
	More...

Accessors
void	enableVelocityStorage ()

void	disableVelocityStorage ()

Public Member Functions inherited from BALL::TrajectoryFile
	TrajectoryFile ()
	Default constructor. More...

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

virtual	~TrajectoryFile ()
	Destructor. More...

bool	operator== (const TrajectoryFile &file) const
	Equality operator. More...

virtual Size	getNumberOfSnapShots ()

Size	getNumberOfAtoms () 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	writeSize_ (const Size &data)

void	writeFloat_ (const float &data)

void	writeVector_ (const vector< Vector3 > &v)

float	readFloat_ ()

Size	readSize_ ()

bool	readSize_ (Size expected_size, const String &what)

bool	readVector_ (vector< Vector3 > &v)

Protected Attributes
Size	verbosity_

bool	swap_bytes_

bool	has_velocities_

bool	charmm_extra_block_A_

bool	charmm_extra_block_B_

String	CORD_

Size	step_number_of_starting_time_

Size	steps_between_saves_

double	time_step_length_

Size	number_of_comments_

Position	current_snapshot_

BinaryFileAdaptor< Size >	adapt_size_

BinaryFileAdaptor< float >	adapt_float_

Protected Attributes inherited from BALL::TrajectoryFile
Size	number_of_snapshots_

Size	number_of_atoms_

Protected Attributes inherited from BALL::File
String	name_

String	original_name_

OpenMode	open_mode_

bool	is_open_

bool	is_temporary_

Private Member Functions
const DCDFile &	operator= (const DCDFile &file)

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

DCD Trajectory file format. This class enables BALL to write DCD files that can be read by VMD. The format stems from the xplor package. This format is NOT portable.

: The header is described in the documentation for the nested DCDHeader class.

: Header of a DCD file: Got this description from http://www.arl.hpc.mil/PET/cta/ccm/software/fmd/Docs/html/fmd_ug.html. Quote: "The exact format of these files is quite ugly, as it reproduces the binary record format of unformatted FORTRAN files. Each such "record" begins with 4 bytes containing the integer value of the number of bytes in the following record. It ends with a record containing the same 4 bytes."

: The header consists of several blocks. Each block starts and ends with the number of bytes enclosed between those numbers, i. e. a block consisting of 8 bytes starts with the number 8 followed by 8 bytes of data and ends with the number 8.

: TODO: complete header description

Definition at line 37 of file DCDFile.h.

Constructor & Destructor Documentation

BALL::DCDFile::DCDFile ( )

Default constructor.

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

Detailed constructor

Exceptions

Exception::FileNotFound if the file could not be openend

virtual BALL::DCDFile::~DCDFile ( )

virtual

Destructor.

Member Function Documentation

virtual bool BALL::DCDFile::append ( const SnapShot & snapshot )

virtual

Append a SnapShot to an existing file. Note that this method does not update the header.

Parameters

snapshot the snapshot we want to save

Returns: true, if writing was successful

Reimplemented from BALL::TrajectoryFile.

virtual void BALL::DCDFile::clear ( )

virtual

Clear method.

Reimplemented from BALL::TrajectoryFile.

void BALL::DCDFile::disableVelocityStorage ( )

void BALL::DCDFile::enableVelocityStorage ( )

virtual bool BALL::DCDFile::flushToDisk ( const std::vector< SnapShot > & buffer )

virtual

Write several SnapShots to disk.

Parameters

buffer a vector of snapshots

Returns: true, if flushing was successful, false ow.

Exceptions

File::CannotWrite if writing to the file failed

Reimplemented from BALL::TrajectoryFile.

bool BALL::DCDFile::hasVelocities ( ) const

bool BALL::DCDFile::init ( )

Initialize this instance, i. e. read the header and update members

bool BALL::DCDFile::isSwappingBytes ( ) const

virtual bool BALL::DCDFile::open	(	const String &	name,
		File::OpenMode	open_mode = `std::ios::in`
	)

virtual

open a DCDFile

Exceptions

Exception::FileNotFound if the file could not be openend

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

private

bool BALL::DCDFile::operator== ( const DCDFile & file ) const

Equality operator.

virtual bool BALL::DCDFile::read ( SnapShot & snapshot )

virtual

Read the next snapshot from the file

Parameters

snapshot a buffer for result delivery

Returns: true, if a snapshot could be read, false ow.

Reimplemented from BALL::TrajectoryFile.

float BALL::DCDFile::readFloat_ ( )

protected

virtual bool BALL::DCDFile::readHeader ( )

virtual

Read the header of an existing file. Return true if the header could be read successfully, false ow.

Reimplemented from BALL::TrajectoryFile.

Size BALL::DCDFile::readSize_ ( )

protected

bool BALL::DCDFile::readSize_	(	Size	expected_size,
		const String &	what
	)

protected

bool BALL::DCDFile::readVector_ ( vector< Vector3 > & v )

protected

virtual bool BALL::DCDFile::seekAndWriteHeader ( )

virtual

void BALL::DCDFile::writeFloat_ ( const float & data )

inlineprotected

Definition at line 148 of file DCDFile.h.

virtual bool BALL::DCDFile::writeHeader ( )

virtual

Write a header Return true if the header could be written successfully, false ow.

Reimplemented from BALL::TrajectoryFile.

void BALL::DCDFile::writeSize_ ( const Size & data )

inlineprotected

Definition at line 144 of file DCDFile.h.

void BALL::DCDFile::writeVector_ ( const vector< Vector3 > & v )

protected

Member Data Documentation

BinaryFileAdaptor<float> BALL::DCDFile::adapt_float_

protected

Definition at line 204 of file DCDFile.h.

BinaryFileAdaptor<Size> BALL::DCDFile::adapt_size_

protected

Definition at line 203 of file DCDFile.h.

bool BALL::DCDFile::charmm_extra_block_A_

protected

Definition at line 176 of file DCDFile.h.

bool BALL::DCDFile::charmm_extra_block_B_

protected

Definition at line 179 of file DCDFile.h.

String BALL::DCDFile::CORD_

protected

Definition at line 182 of file DCDFile.h.

Position BALL::DCDFile::current_snapshot_

protected

Definition at line 201 of file DCDFile.h.

bool BALL::DCDFile::has_velocities_

protected

Definition at line 173 of file DCDFile.h.

Size BALL::DCDFile::number_of_comments_

protected

Definition at line 194 of file DCDFile.h.

Size BALL::DCDFile::step_number_of_starting_time_

protected

Definition at line 185 of file DCDFile.h.

Size BALL::DCDFile::steps_between_saves_

protected

Definition at line 188 of file DCDFile.h.

bool BALL::DCDFile::swap_bytes_

protected

Definition at line 170 of file DCDFile.h.

double BALL::DCDFile::time_step_length_

protected

Definition at line 191 of file DCDFile.h.

Size BALL::DCDFile::verbosity_

protected

Definition at line 167 of file DCDFile.h.

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation