TrajectoryFile Class Reference
[Molecular Dynamics Trajectory File Formats]

Trajectory file format for MD simulation. More...

#include <trajectoryFile.h>

Inheritance diagram for TrajectoryFile:

List of all members.

Public Member Functions
Constructors and Destructor
	TrajectoryFile () throw ()
	Default constructor.
	TrajectoryFile (const TrajectoryFile &file) throw ()
	Copy constructor.
	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.
virtual	~TrajectoryFile () throw ()
	Destructor.
Assignment
const TrajectoryFile &	operator= (const TrajectoryFile &file) throw ()
	Assignment operator.
virtual void	clear () throw ()
	Clear method.
Predicates
bool	operator== (const TrajectoryFile &file) const throw ()
	Equality operator.
Accessors
Size	getNumberOfSnapShots () const throw ()
	get the number of snapshots stored in this instance.
Size	getNumberOfAtoms () const throw ()
	get the number of atoms coverd by each snapshot.
Public methods for file handling
virtual bool	readHeader () throw ()
	Read the header of an existing file.
virtual bool	writeHeader () throw ()
	Write a header.
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 bool	flushToDisk (const std::vector< SnapShot > &buffer) throw (File::CannotWrite)
	Write several SnapShots to disk.
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

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

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Member Function Documentation

virtual bool TrajectoryFile::append (  const SnapShot &  snapshot  )  throw () [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 DCDFile, and TRRFile.

virtual bool 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 DCDFile, and TRRFile.

Size TrajectoryFile::getNumberOfAtoms (   )  const throw ()

get the number of atoms coverd by each snapshot. Returns: the number of atoms

Size TrajectoryFile::getNumberOfSnapShots (   )  const throw ()

get the number of snapshots stored in this instance. Returns: the number of snapshots of this instance

virtual bool TrajectoryFile::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 ow. Reimplemented in DCDFile, and TRRFile.

virtual bool TrajectoryFile::readHeader (   )  throw () [virtual]

Read the header of an existing file. Returns: true if the header could be read successfully, false ow. Reimplemented in DCDFile.

virtual bool TrajectoryFile::writeHeader (   )  throw () [virtual]

Write a header. Returns: true if the header could be written successfully, false ow. Reimplemented in DCDFile.