DCDFile Class Reference
[Molecular Dynamics Trajectory File Formats]

DCD Trajectory file format. More...

#include <DCDFile.h>

Inheritance diagram for DCDFile:

List of all members.

Public Member Functions
Constructors and Destructor
	DCDFile () throw ()
	Default constructor.
	DCDFile (const DCDFile &file) throw (Exception::FileNotFound)
	Copy constructor.
	DCDFile (const String &name, File::OpenMode open_mode=std::ios::in) throw (Exception::FileNotFound)
	Detailed constructor.
virtual	~DCDFile () throw ()
	Destructor.
Assignment
const DCDFile &	operator= (const DCDFile &file) throw ()
	Assignment operator.
virtual void	clear () throw ()
	Clear method.
Predicates
bool	operator== (const DCDFile &file) const throw ()
	Equality operator.
bool	isSwappingBytes () const throw ()
bool	hasVelocities () const throw ()
Public methods for file handling
virtual bool	open (const String &name, File::OpenMode open_mode=std::ios::in) throw (Exception::FileNotFound)
	open a DCDFile
bool	init () throw ()
	Initialize this instance, i.
virtual bool	readHeader () throw ()
	Read the header of an existing file.
virtual bool	writeHeader () throw ()
	Write a header Return true if the header could be written successfully, false ow.
virtual bool	seekAndWriteHeader () throw ()
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.
Accessors
void	enableVelocityStorage () throw ()
void	disableVelocityStorage () throw ()
Protected Member Functions
void	writeSize_ (const Size &data) throw ()
void	writeFloat_ (const float &data) throw ()
void	writeVector_ (const vector< Vector3 > &v) throw ()
float	readFloat_ () throw ()
Size	readSize_ () throw ()
bool	readSize_ (Size expected_size, const String &what) throw ()
bool	readVector_ (vector< Vector3 > &v) throw ()
Protected Attributes
Size	verbosity_
bool	swap_bytes_
bool	has_velocities_
bool	charmm_extra_block_A_
bool	charmm_extra_block_B_
String	CORD_
Size	step_number_of_starting_time_
Size	steps_between_saves_
double	time_step_length_
Size	number_of_comments_
Position	current_snapshot_
BinaryFileAdaptor< Size >	adapt_size_
BinaryFileAdaptor< float >	adapt_float_

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Detailed Description

DCD Trajectory file format.

This class enables BALL to write DCD files that can be read by VMD. The format stems from the xplor package. This format is NOT portable.

The header is described in the documentation for the nested DCDHeader class.

Header of a DCD file: Got this description from http://www.arl.hpc.mil/PET/cta/ccm/software/fmd/Docs/html/fmd_ug.html. Quote: "The exact format of these files is quite ugly, as it reproduces the binary record format of unformatted FORTRAN files. Each such "record" begins with 4 bytes containing the integer value of the number of bytes in the following record. It ends with a record containing the same 4 bytes."

The header consists of several blocks. Each block starts and ends with the number of bytes enclosed between those numbers, i. e. a block consisting of 8 bytes starts with the number 8 followed by 8 bytes of data and ends with the number 8.

TODO: complete header description

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Member Function Documentation

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

Append a SnapShot to an existing file. Note that this method does not update the header. Parameters: snapshot  the snapshot we want to save Returns: true, if writing was successful Reimplemented from TrajectoryFile.

virtual bool DCDFile::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.

bool DCDFile::init (   )  throw ()

Initialize this instance, i. e. read the header and update members

virtual bool DCDFile::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 from TrajectoryFile.

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

Read the header of an existing file. Return true if the header could be read successfully, false ow. Reimplemented from TrajectoryFile.

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

Write a header Return true if the header could be written successfully, false ow. Reimplemented from TrajectoryFile.