TRRFile Class Reference
[Molecular Dynamics Trajectory File Formats]

TRR Trajectory file format. More...

#include <TRRFile.h>

Inheritance diagram for TRRFile:

List of all members.

Public Member Functions
Constructors and Destructor
	TRRFile () throw ()
	Default constructor.
	TRRFile (const TRRFile &file) throw (Exception::FileNotFound)
	Copy constructor.
	TRRFile (const String &name, File::OpenMode open_mode=std::ios::in) throw ()
	Construct and open a file.
virtual	~TRRFile () throw ()
	Destructor.
Assignment
const TRRFile &	operator= (const TRRFile &file) throw ()
	Assignment operator.
virtual void	clear () throw ()
	Clear method.
Predicates
bool	operator== (const TRRFile &file) const throw ()
	Equality operator.
Public methods for file handling
virtual bool	init () throw ()
	Initialize the file for usage.
virtual bool	writeNextHeader (const TRRHeader &header) throw ()
	Writes the next header that shall preceed the next data block.
virtual bool	readNextHeader (TRRHeader &header) throw ()
	Reads the next header preceding the next data block.
virtual bool	append (const SnapShot &snapshot) throw ()
	Append a SnapShot to an existing file.
virtual bool	read (SnapShot &snapshot) throw ()
	Read the next snapshot from the file.
virtual TRRFile &	operator>> (SnapShotManager &ssm) throw ()
	Read the whole file into a SnapShotManager.
virtual bool	flushToDisk (const std::vector< SnapShot > &buffer) throw (File::CannotWrite)
	Write several SnapShots to disk.
Accessors
bool	hasVelocities () const throw ()
void	setVelocityStorage (bool storage) throw ()
bool	hasForces () const throw ()
void	setForceStorage (bool storage) throw ()
Size	getPrecision () const throw ()
bool	setPrecision (const Size precision) throw ()
float	getTimestep () const throw ()
void	setTimestep (float timestep) throw ()
Vector3	getBoundingBoxX () const throw ()
Vector3	getBoundingBoxY () const throw ()
Vector3	getBoundingBoxZ () const throw ()
void	setBoundingBox (const Vector3 &x, const Vector3 &y, const Vector3 &z) throw ()
Protected Attributes
TRRHeader	header_
Size	precision_
bool	has_velocities_
bool	has_forces_
Size	timestep_index_
float	timestep_
Vector3	box1_
Vector3	box2_
Vector3	box3_

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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.

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Member Function Documentation

virtual bool TRRFile::append (  const SnapShot &  snapshot  )  throw () [virtual]

Append a SnapShot to an existing file. Parameters: snapshot  the SnapShot we want to store Returns: true, if writing was successful Reimplemented from TrajectoryFile.

virtual bool 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 TrajectoryFile.

virtual bool TRRFile::read (  SnapShot &  snapshot  )  throw () [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 TrajectoryFile.

virtual bool TRRFile::readNextHeader (  TRRHeader &  header  )  throw () [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.

virtual bool TRRFile::writeNextHeader (  const TRRHeader &  header  )  throw () [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.