BALL::TRRFile Class Reference
[Molecular Dynamics Trajectory File Formats]

#include <BALL/FORMAT/TRRFile.h>

Inheritance diagram for BALL::TRRFile:

List of all members.

Classes
class	TRRHeader
Public Member Functions
Constructors and Destructor
	TRRFile ()
	Default constructor.
	TRRFile (const TRRFile &file) throw (Exception::FileNotFound)
	Copy constructor.
	TRRFile (const String &name, File::OpenMode open_mode=std::ios::in)
	Construct and open a file.
virtual	~TRRFile ()
	Destructor.
Assignment
const TRRFile &	operator= (const TRRFile &file)
	Assignment operator.
virtual void	clear ()
	Clear method.
Predicates
bool	operator== (const TRRFile &file) const
	Equality operator.
Public methods for file handling
virtual bool	init ()
	Initialize the file for usage.
virtual bool	writeNextHeader (const TRRHeader &header)
virtual bool	readNextHeader (TRRHeader &header)
virtual bool	append (const SnapShot &snapshot)
virtual bool	read (SnapShot &snapshot)
virtual TRRFile &	operator>> (SnapShotManager &ssm)
	Read the whole file into a SnapShotManager.
virtual bool	flushToDisk (const std::vector< SnapShot > &buffer) throw (File::CannotWrite)
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)
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_

---

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.

---

Constructor & Destructor Documentation

BALL::TRRFile::TRRFile

(

)

Default constructor.

BALL::TRRFile::TRRFile

(

const TRRFile &

file

)

throw (Exception::FileNotFound)

Copy 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

)

throw (File::CannotWrite) [virtual]

Write several SnapShots to disk.

Parameters:

buffer

a vector of snapshots

Returns:

true, if flushing was successful, false ow.

Reimplemented from BALL::TrajectoryFile.

Vector3 BALL::TRRFile::getBoundingBoxX

(

)

const

Vector3 BALL::TRRFile::getBoundingBoxY

(

)

const

Vector3 BALL::TRRFile::getBoundingBoxZ

(

)

const

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

)

Assignment operator.

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::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::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]

BinaryFileAdaptor<double> BALL::TRRFile::adapt_double_ [protected]

BinaryFileAdaptor<float> BALL::TRRFile::adapt_float_ [protected]

BinaryFileAdaptor<Size> BALL::TRRFile::adapt_size_ [protected]

Vector3 BALL::TRRFile::box1_ [protected]

Vector3 BALL::TRRFile::box2_ [protected]

Vector3 BALL::TRRFile::box3_ [protected]

bool BALL::TRRFile::has_forces_ [protected]

bool BALL::TRRFile::has_velocities_ [protected]

TRRHeader BALL::TRRFile::header_ [protected]

Size BALL::TRRFile::precision_ [protected]

float BALL::TRRFile::timestep_ [protected]

Size BALL::TRRFile::timestep_index_ [protected]