#include <BALL/FORMAT/TRRFile.h>

Inheritance diagram for BALL::TRRFile:

Classes
class	TRRHeader

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

	TRRFile (const String &name, File::OpenMode open_mode=std::ios::in)
	Construct and open a file. More...

virtual	~TRRFile ()
	Destructor. More...

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

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

Public methods for file handling
virtual bool	init ()
	Initialize the file for usage. More...

virtual bool	readHeader ()

virtual bool	writeNextHeader (const TRRHeader &header)

virtual bool	readNextHeader (TRRHeader &header)

virtual bool	append (const SnapShot &snapshot)

virtual bool	read (SnapShot &snapshot)

virtual bool	skipFrame ()

virtual Size	getNumberOfSnapShots ()

virtual TRRFile &	operator>> (SnapShotManager &ssm)
	Read the whole file into a SnapShotManager. More...

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

Accessors
bool	hasVelocities () const

void	setVelocityStorage (bool storage)

bool	hasForces () const

void	setForceStorage (bool storage)

Size	getPrecision () const

bool	setPrecision (const Size precision)

float	getTimestep () const

void	setTimestep (float timestep)

Vector3	getBoundingBoxX () const

Vector3	getBoundingBoxY () const

Vector3	getBoundingBoxZ () const

void	setBoundingBox (const Vector3 &x, const Vector3 &y, const Vector3 &z)

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...

Size	getNumberOfAtoms () const

virtual bool	writeHeader ()

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

Static Public Attributes
static const double	to_angstrom

static const double	to_nanometer

Protected Attributes
TRRHeader	header_

Size	precision_

bool	has_velocities_

bool	has_forces_

Size	timestep_index_

float	timestep_

Vector3	box1_

Vector3	box2_

Vector3	box3_

BinaryFileAdaptor< Size >	adapt_size_

BinaryFileAdaptor< char >	adapt_char_

BinaryFileAdaptor< float >	adapt_float_

BinaryFileAdaptor< double >	adapt_double_

Size	old_file_size_

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 TRRFile &	operator= (const TRRFile &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 Protected Attributes inherited from BALL::File
static HashSet< String >	created_temp_filenames_

static TransformationManager	transformation_manager_

static Size	transformation_methods_

Detailed Description

TRR Trajectory file format. This class enables BALL to read and write GROMACS TRR files. This format is portable.

: In a TRR file, each timestep is preceded by a header. The header is handled by the nested TRRHeader class.

Definition at line 28 of file TRRFile.h.

Constructor & Destructor Documentation

BALL::TRRFile::TRRFile ( )

Default constructor.

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

Construct and open a file.

virtual BALL::TRRFile::~TRRFile ( )

virtual

Destructor.

Member Function Documentation

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

virtual

Append a SnapShot to an existing file

Parameters

snapshot the SnapShot we want to store

Returns: true, if writing was successful

Reimplemented from BALL::TrajectoryFile.

virtual void BALL::TRRFile::clear ( )

virtual

Clear method.

Reimplemented from BALL::TrajectoryFile.

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

virtual

Flush the SnapShot buffer to disk.

Exceptions

File::CannotWrite if writing to the file failed

Reimplemented from BALL::TrajectoryFile.

Vector3 BALL::TRRFile::getBoundingBoxX ( ) const

Vector3 BALL::TRRFile::getBoundingBoxY ( ) const

Vector3 BALL::TRRFile::getBoundingBoxZ ( ) const

virtual Size BALL::TRRFile::getNumberOfSnapShots ( )

virtual

get the number of snapshots stored in this instance.

Returns: the number of snapshots of this instance

Reimplemented from BALL::TrajectoryFile.

Size BALL::TRRFile::getPrecision ( ) const

float BALL::TRRFile::getTimestep ( ) const

bool BALL::TRRFile::hasForces ( ) const

bool BALL::TRRFile::hasVelocities ( ) const

virtual bool BALL::TRRFile::init ( )

virtual

Initialize the file for usage.

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

private

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

Equality operator.

virtual TRRFile& BALL::TRRFile::operator>> ( SnapShotManager & ssm )

virtual

Read the whole file into a SnapShotManager.

virtual bool BALL::TRRFile::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 otherwise.

Reimplemented from BALL::TrajectoryFile.

virtual bool BALL::TRRFile::readHeader ( )

virtual

Read file header This function is actually a nop, since TRRFiles don't have file headers; it is only provided for interface reasons.

Reimplemented from BALL::TrajectoryFile.

virtual bool BALL::TRRFile::readNextHeader ( TRRHeader & header )

virtual

Reads the next header preceding the next data block.

Parameters

header a buffer for result delivery

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

void BALL::TRRFile::setBoundingBox	(	const Vector3 &	x,
		const Vector3 &	y,
		const Vector3 &	z
	)

void BALL::TRRFile::setForceStorage ( bool storage )

bool BALL::TRRFile::setPrecision ( const Size precision )

void BALL::TRRFile::setTimestep ( float timestep )

void BALL::TRRFile::setVelocityStorage ( bool storage )

virtual bool BALL::TRRFile::skipFrame ( )

virtual

Skip the next snapshot in the file

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

virtual bool BALL::TRRFile::writeNextHeader ( const TRRHeader & header )

virtual

Writes the next header that shall preceed the next data block.

Parameters

header the TRRHeader we want to write

Returns: true, if a header could be written, false ow.

Member Data Documentation

BinaryFileAdaptor<char> BALL::TRRFile::adapt_char_

protected

Definition at line 315 of file TRRFile.h.

BinaryFileAdaptor<double> BALL::TRRFile::adapt_double_

protected

Definition at line 317 of file TRRFile.h.

BinaryFileAdaptor<float> BALL::TRRFile::adapt_float_

protected

Definition at line 316 of file TRRFile.h.

BinaryFileAdaptor<Size> BALL::TRRFile::adapt_size_

protected

Definition at line 314 of file TRRFile.h.

Vector3 BALL::TRRFile::box1_

protected

Definition at line 312 of file TRRFile.h.

Vector3 BALL::TRRFile::box2_

protected

Definition at line 312 of file TRRFile.h.

Vector3 BALL::TRRFile::box3_

protected

Definition at line 312 of file TRRFile.h.

bool BALL::TRRFile::has_forces_

protected

Definition at line 302 of file TRRFile.h.

bool BALL::TRRFile::has_velocities_

protected

Definition at line 299 of file TRRFile.h.

TRRHeader BALL::TRRFile::header_

protected

Definition at line 293 of file TRRFile.h.

Size BALL::TRRFile::old_file_size_

protected

Definition at line 319 of file TRRFile.h.

Size BALL::TRRFile::precision_

protected

Definition at line 296 of file TRRFile.h.

float BALL::TRRFile::timestep_

protected

Definition at line 308 of file TRRFile.h.

Size BALL::TRRFile::timestep_index_

protected

Definition at line 305 of file TRRFile.h.

const double BALL::TRRFile::to_angstrom

static

Definition at line 33 of file TRRFile.h.

const double BALL::TRRFile::to_nanometer

static

Definition at line 34 of file TRRFile.h.

Classes

Public Member Functions

Static Public Attributes

Protected Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation