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

#include <BALL/FORMAT/trajectoryFile.h>

Inheritance diagram for BALL::TrajectoryFile:

List of all members.

Public Member Functions
Constructors and Destructor
	TrajectoryFile ()
	Default constructor.
	TrajectoryFile (const TrajectoryFile &file)
	Copy constructor.
	TrajectoryFile (const String &filename, File::OpenMode open_mode=std::ios::in) throw (Exception::FileNotFound)
virtual	~TrajectoryFile ()
	Destructor.
Assignment
const TrajectoryFile &	operator= (const TrajectoryFile &file)
	Assignment operator.
virtual void	clear ()
	Clear method.
Predicates
bool	operator== (const TrajectoryFile &file) const
	Equality operator.
Accessors
Size	getNumberOfSnapShots () const
Size	getNumberOfAtoms () const
Public methods for file handling
virtual bool	readHeader ()
virtual bool	writeHeader ()
virtual bool	append (const SnapShot &snapshot)
virtual bool	read (SnapShot &snapshot)
virtual bool	flushToDisk (const std::vector< SnapShot > &buffer) throw (File::CannotWrite)
Protected Attributes
Size	number_of_snapshots_
Size	number_of_atoms_

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Detailed Description

Trajectory file format for MD simulation. This is more an interface definition than an actual class, because it would not make too much sense to create yet-another-trajectory-format. This class will be specialized by actual formats, like DCD.

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Constructor & Destructor Documentation

BALL::TrajectoryFile::TrajectoryFile

(

)

Default constructor.

BALL::TrajectoryFile::TrajectoryFile

(

const TrajectoryFile &

file

)

Copy constructor.

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

Detailed constructor requiring a filename and the mode in which this file should be opened.

See also:

File

Parameters:

	filename	the name of the file
	open_mode	the mode in which this file should be opened

virtual BALL::TrajectoryFile::~TrajectoryFile

(

)

[virtual]

Destructor.

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Member Function Documentation

virtual bool BALL::TrajectoryFile::append

(

const SnapShot &

snapshot

)

[virtual]

Append a SnapShot to an existing file. Note that this method does note update the header.

Parameters:

snapshot

the SnapShot we want to save

Returns:

true, if writing was successful

Reimplemented in BALL::DCDFile, and BALL::TRRFile.

virtual void BALL::TrajectoryFile::clear

(

)

[virtual]

Clear method.

Reimplemented from BALL::File.

Reimplemented in BALL::DCDFile, and BALL::TRRFile.

virtual bool BALL::TrajectoryFile::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 in BALL::DCDFile, and BALL::TRRFile.

Size BALL::TrajectoryFile::getNumberOfAtoms

(

)

const

get the number of atoms coverd by each snapshot.

Returns:

the number of atoms

Size BALL::TrajectoryFile::getNumberOfSnapShots

(

)

const

get the number of snapshots stored in this instance.

Returns:

the number of snapshots of this instance

const TrajectoryFile& BALL::TrajectoryFile::operator=

(

const TrajectoryFile &

file

)

Assignment operator.

bool BALL::TrajectoryFile::operator==

(

const TrajectoryFile &

file

)

const

Equality operator.

virtual bool BALL::TrajectoryFile::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 in BALL::DCDFile, and BALL::TRRFile.

virtual bool BALL::TrajectoryFile::readHeader

(

)

[virtual]

Read the header of an existing file.

Returns:

true if the header could be read successfully, false ow.

Reimplemented in BALL::DCDFile.

virtual bool BALL::TrajectoryFile::writeHeader

(

)

[virtual]

Write a header.

Returns:

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

Reimplemented in BALL::DCDFile.

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Member Data Documentation

Size BALL::TrajectoryFile::number_of_atoms_ [protected]

Size BALL::TrajectoryFile::number_of_snapshots_ [protected]