BALL
DCDFile

#include <BALL/FORMAT/DCDFile.h>

Inheritance diagram for BALL::DCDFile:

List of all members.

Public Member Functions
Constructors and Destructor
	DCDFile ()
	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 ()
	Destructor.
Assignment
const DCDFile &	operator= (const DCDFile &file)
	Assignment operator.
virtual void	clear ()
	Clear method.
Predicates
bool	operator== (const DCDFile &file) const
	Equality operator.
bool	isSwappingBytes () const
bool	hasVelocities () const
Public methods for file handling
virtual bool	open (const String &name, File::OpenMode open_mode=std::ios::in) throw (Exception::FileNotFound)
bool	init ()
virtual bool	readHeader ()
virtual bool	writeHeader ()
virtual bool	seekAndWriteHeader ()
virtual bool	append (const SnapShot &snapshot)
virtual bool	read (SnapShot &snapshot)
virtual bool	flushToDisk (const std::vector< SnapShot > &buffer) throw (File::CannotWrite)
Accessors
void	enableVelocityStorage ()
void	disableVelocityStorage ()
Protected Member Functions
void	writeSize_ (const Size &data)
void	writeFloat_ (const float &data)
void	writeVector_ (const vector< Vector3 > &v)
float	readFloat_ ()
Size	readSize_ ()
bool	readSize_ (Size expected_size, const String &what)
bool	readVector_ (vector< Vector3 > &v)
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_

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

Constructor & Destructor Documentation

BALL::DCDFile::DCDFile ( )

Default constructor.

BALL::DCDFile::DCDFile ( const DCDFile & file ) throw (Exception::FileNotFound)

Copy constructor.

BALL::DCDFile::DCDFile	(	const String &	name,
		File::OpenMode	open_mode = `std::ios::in`
	)		throw (Exception::FileNotFound)

Detailed constructor.

virtual BALL::DCDFile::~DCDFile ( ) [virtual]

Destructor.

Member Function Documentation

virtual bool BALL::DCDFile::append ( const SnapShot & snapshot ) [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 BALL::TrajectoryFile.

virtual void BALL::DCDFile::clear ( ) [virtual]

Clear method.

Reimplemented from BALL::TrajectoryFile.

void BALL::DCDFile::disableVelocityStorage ( )

void BALL::DCDFile::enableVelocityStorage ( )

virtual bool BALL::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 BALL::TrajectoryFile.

bool BALL::DCDFile::hasVelocities ( ) const

bool BALL::DCDFile::init ( )

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

bool BALL::DCDFile::isSwappingBytes ( ) const

virtual bool BALL::DCDFile::open	(	const String &	name,
		File::OpenMode	open_mode = `std::ios::in`
	)		throw (Exception::FileNotFound) `[virtual]`

open a DCDFile

Reimplemented from BALL::File.

const DCDFile& BALL::DCDFile::operator= ( const DCDFile & file )

Assignment operator.

bool BALL::DCDFile::operator== ( const DCDFile & file ) const

Equality operator.

virtual bool BALL::DCDFile::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 from BALL::TrajectoryFile.

float BALL::DCDFile::readFloat_ ( ) [protected]

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

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

Reimplemented from BALL::TrajectoryFile.

Size BALL::DCDFile::readSize_ ( ) [protected]

bool BALL::DCDFile::readSize_	(	Size	expected_size,
		const String &	what
	)		`[protected]`

bool BALL::DCDFile::readVector_ ( vector< Vector3 > & v ) [protected]

virtual bool BALL::DCDFile::seekAndWriteHeader ( ) [virtual]

void BALL::DCDFile::writeFloat_ ( const float & data ) [inline, protected]

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

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

Reimplemented from BALL::TrajectoryFile.

void BALL::DCDFile::writeSize_ ( const Size & data ) [inline, protected]

void BALL::DCDFile::writeVector_ ( const vector< Vector3 > & v ) [protected]

Member Data Documentation

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

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

bool BALL::DCDFile::charmm_extra_block_A_ [protected]

bool BALL::DCDFile::charmm_extra_block_B_ [protected]

String BALL::DCDFile::CORD_ [protected]

Position BALL::DCDFile::current_snapshot_ [protected]

bool BALL::DCDFile::has_velocities_ [protected]

Size BALL::DCDFile::number_of_comments_ [protected]

Size BALL::DCDFile::step_number_of_starting_time_ [protected]

Size BALL::DCDFile::steps_between_saves_ [protected]

bool BALL::DCDFile::swap_bytes_ [protected]

double BALL::DCDFile::time_step_length_ [protected]

Size BALL::DCDFile::verbosity_ [protected]