loos::DCD Class Reference

Class for reading DCD files. More...

#include <dcd.hpp>

Inheritance diagram for loos::DCD:

Collaboration diagram for loos::DCD:

Classes
class	EndOfFile

Public Member Functions
	DCD (const std::string s)
	Begin reading from the file named s.
	DCD (const char *s)
	Begin reading from the file named s.
	DCD (std::istream &fs)
	Begin reading from the stream ifs.
std::string	description () const
	Return a string describing trajectory format.
virtual uint	natoms (void) const
virtual bool	hasPeriodicBox (void) const
virtual GCoord	periodicBox (void) const
	Returns the periodic box for the current frame/trajectory.
virtual bool	hasVelocities () const
	Whether or not the trajectory format supports velocities.
virtual double	velocityConversionFactor () const
	Conversion applied to velocities to get to \AA/ps.
std::vector< std::string >	titles (void) const
int	icntrl (const int) const
void	icntrl (const int, const int)
std::vector< double >	crystalParams (void) const
bool	hasCrystalParams (void) const
virtual float	timestep (void) const
	Timestep per frame.
virtual uint	nframes (void) const
	Number of frames in the trajectory.
std::vector< dcd_real >	xcoords (void) const
	Return the raw coords...
std::vector< dcd_real >	ycoords (void) const
	Return the raw coords...
std::vector< dcd_real >	zcoords (void) const
	Return the raw coords...
unsigned int	nsteps (void) const
float	delta (void) const
int	nsavc (void) const
int	nfile (void) const
int	nfixed (void) const
bool	nativeFormat (void) const
	Returns true if the DCD file being read is in the native endian format.
virtual std::vector< GCoord >	coords (void) const
	Auto-interleave the coords into a vector of GCoord()'s.
std::vector< GCoord >	mappedCoords (const std::vector< int > &map)
	Interleave coords, selecting entries indexed by map.
virtual bool	parseFrame (void)
	Parse a frame of the DCD.
Public Member Functions inherited from loos::Trajectory
	Trajectory (const std::string &s)
	Automatically open the file named s.
	Trajectory (std::istream &fs)
	Open using the given stream...
	Trajectory (const Trajectory &t)
virtual std::string	filename () const
	Return the stored filename.
bool	rewind (void)
	Rewinds the readFrame() iterator.
void	updateGroupCoords (AtomicGroup &g)
	Update the coordinates in an AtomicGroup with the current frame.
virtual std::vector< GCoord >	velocities (void) const
	Returns the current frame's velocities as a vector of GCoords.
void	updateGroupVelocities (AtomicGroup &g)
void	seekNextFrame (void)
void	seekFrame (const uint i)
bool	readFrame (void)
	Reads the next frame in a trajectory, returning false if at the end.
bool	readFrame (const int i)
	Reads a specific frame in a trajectory.
bool	atEnd () const
uint	currentFrame () const

Static Public Member Functions
static pTraj	create (const std::string &fname, const AtomicGroup &model)
static void	setSuppression (const bool b)

Additional Inherited Members
Public Types inherited from loos::Trajectory
typedef boost::shared_ptr< std::istream >	pStream
Protected Member Functions inherited from loos::Trajectory
void	setInputStream (const std::string &fname)
void	setInputStream (std::istream &fs)
Protected Attributes inherited from loos::Trajectory
pStream	ifs
bool	cached_first
std::string	_filename
uint	_current_frame

Detailed Description

Class for reading DCD files.

Instantiating a DCD object with either a filename or an fstream only reads the header from the file, not any frames. When a frame is read, the x,y,z coordinates are stored internally in a vector. This must be copied out to the caller or used to update the coordinates for an AtomicGroup.

Notes:

• Does NOT support fixed atoms
• Does NOT support velocity format
• Reorders the crystal parameters (if present) so they are in a more sensible order (i.e. a, b, c, alpha, beta, gamma)
• [Almost] everything returned is a copy
• Endian detection is based on the expected size of the header

Member Function Documentation

coords()

std::vector< GCoord > loos::DCD::coords ( void ) const

virtual

Auto-interleave the coords into a vector of GCoord()'s.

This can be a pretty slow operation, so be careful.

Implements loos::Trajectory.

description()

std::string loos::DCD::description ( ) const

inlinevirtual

Return a string describing trajectory format.

Reimplemented from loos::Trajectory.

hasPeriodicBox()

bool loos::DCD::hasPeriodicBox ( void ) const

virtual

Tests whether or not the given frame/trajectory has periodic boundary information. The presence of periodic box information does not necessarily indicate that said information has been read in yet. For example, the presence of crystal data is in the header so this can be detected before any frame is read, but the crystal data itself is only read when a frame is read in.

Implements loos::Trajectory.

hasVelocities()

virtual bool loos::DCD::hasVelocities ( void ) const

inlinevirtual

Whether or not the trajectory format supports velocities.

Reimplemented from loos::Trajectory.

natoms()

uint loos::DCD::natoms ( void ) const

virtual

of atoms per frame

Implements loos::Trajectory.

nframes()

uint loos::DCD::nframes ( void ) const

virtual

Number of frames in the trajectory.

Implements loos::Trajectory.

parseFrame()

bool loos::DCD::parseFrame ( void )

virtual

Parse a frame of the DCD.

Implements loos::Trajectory.

periodicBox()

GCoord loos::DCD::periodicBox ( void ) const

virtual

Returns the periodic box for the current frame/trajectory.

Implements loos::Trajectory.

timestep()

float loos::DCD::timestep ( void ) const

virtual

Timestep per frame.

Implements loos::Trajectory.

velocityConversionFactor()

virtual double loos::DCD::velocityConversionFactor ( ) const

inlinevirtual

Conversion applied to velocities to get to \AA/ps.

Reimplemented from loos::Trajectory.

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

• src/dcd.hpp
• src/dcd.cpp