loos::DCDWriter Class Reference

A very lightweight class for writing simple DCDs. More...

#include <dcdwriter.hpp>

Inheritance diagram for loos::DCDWriter:

Collaboration diagram for loos::DCDWriter:

Public Member Functions
	DCDWriter (const std::string &s, const bool append=false)
	Setup for writing to a file named by s.
	DCDWriter (std::iostream &fs, const bool append=false)
	Setup for writing to a stream.
	DCDWriter (const std::string &s, const std::vector< AtomicGroup > &grps, const bool append=false)
	Writes the coordinates of grps to file s as a DCD.
	DCDWriter (const std::string &s, const std::vector< AtomicGroup > &grps, const std::string &comment, const bool append=false)
	Writes coordinates of grps adding comment as a TITLE record.
	DCDWriter (const std::string &s, const std::vector< AtomicGroup > &grps, const std::vector< std::string > &comments, const bool append=false)
	Writes coordinates of grps adding comments as TITLE records.
void	setHeader (const int na, const int ns, const greal ts, const bool bf)
	Sets header parameters.
void	setTitles (const std::vector< std::string > &titles)
void	setTitle (const std::string &s)
void	addTitle (const std::string &s)
void	setComments (const std::vector< std::string > &comments)
	Set comments in metadata (not all formats support)
bool	hasComments () const
	Does format support comments in metadata?
void	writeFrame (const AtomicGroup &grp)
	Writes a frame to a growing DCD.
void	writeFrames (const std::vector< AtomicGroup > &grps)
	Same as writeFrame(), but writes out the vector of frames...
void	writeHeader (void)
uint	framesWritten (void) const
	Total frames in output file.
Public Member Functions inherited from loos::TrajectoryWriter
	TrajectoryWriter (const std::string &fname, const bool append=false)
	Write a trajectory to a file, optionally appending.
	TrajectoryWriter (std::iostream *s, const bool append=false)
	Write a trajectory to a stream.
virtual void	setComments (const std::string &s)
	Set comment in metadata (not all formats support)
virtual void	writeFrame (const AtomicGroup &model, const uint step, const double time)
	Write a single frame specifying the step and timepoint.
virtual bool	hasFrameStep () const
	Can format write step on a per-frame basis?
virtual bool	hasFrameTime () const
	Can format write time on a per-frame basis?
bool	isAppending () const
	Returns true if appending to an existing trajectory.

Static Public Member Functions
static pTrajectoryWriter	create (const std::string &s, const bool append=false)

Additional Inherited Members
Protected Attributes inherited from loos::TrajectoryWriter
std::iostream *	stream_
std::string	_filename
bool	appending_
bool	delete_

Detailed Description

A very lightweight class for writing simple DCDs.

Constructor & Destructor Documentation

DCDWriter()

loos::DCDWriter::DCDWriter ( const std::string & s, const bool append = false )

inlineexplicit

Setup for writing to a file named by s.

You can opt to write the header explicitly, i.e.

DCDWriter dcd("output.dcd");
dcd.setHeader(500, 10, 1e-3, no);
dcd.setTitles("MY TITLE HERE");
dcd.writeHeader();
dcd.writeFrame(frame);

Or you can let dcdwriter create the header from the first frame written...

Member Function Documentation

framesWritten()

uint loos::DCDWriter::framesWritten ( void ) const

inlinevirtual

Total frames in output file.

For files being appended too, this includes the frames already written...

Implements loos::TrajectoryWriter.

hasComments()

bool loos::DCDWriter::hasComments ( ) const

inlinevirtual

Does format support comments in metadata?

Reimplemented from loos::TrajectoryWriter.

setComments()

void loos::DCDWriter::setComments ( const std::vector< std::string > & comments )

inlinevirtual

Set comments in metadata (not all formats support)

Reimplemented from loos::TrajectoryWriter.

setHeader()

void loos::DCDWriter::setHeader ( const int na, const int ns, const greal ts, const bool bf )

inline

Sets header parameters.

These must be set prior to writing a header or frame, but it is not an error to not do so... Arguments:

• na Number of atoms
• ns Number of steps (total frames)
• ts Timestep of each frame
• bf Flag for whether or not each frame will include periodic box info as Xtal data

writeFrame()

void loos::DCDWriter::writeFrame ( const AtomicGroup & grp )

virtual

Writes a frame to a growing DCD.

writeFrame() will automatically extend the DCD for you if you write past the initially specified number of frames. Alternatively, you can just begin writing frames without explicitly writing a header and let writeFrame() handle it for you. As the DCD grows, writeFrame() will automatically update the header information for you.

Implements loos::TrajectoryWriter.

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The documentation for this class was generated from the following files:

• src/dcdwriter.hpp
• src/dcdwriter.cpp