loos::TRR Class Reference

Class representing the GROMACS TRR trajectory files. More...

#include <trr.hpp>

Inheritance diagram for loos::TRR:

Collaboration diagram for loos::TRR:

Public Member Functions
	TRR (const std::string &s)
	TRR (const char *p)
	TRR (std::istream &is)
std::string	description () const
	Return a string describing trajectory format.
uint	natoms (void) const
float	timestep (void) const
uint	nframes (void) const
	Number of frames in the trajectory.
bool	hasPeriodicBox (void) const
GCoord	periodicBox (void) const
	Returns the periodic box for the current frame/trajectory.
std::vector< GCoord >	coords (void) const
	Returns the current frames coordinates as a vector of GCoords.
std::vector< double >	virial (void) const
std::vector< double >	pressure (void) const
std::vector< GCoord >	forces (void) const
bool	isDouble (void) const
bool	hasVirial (void) const
bool	hasPressure (void) const
bool	hasCoords (void) const
bool	hasVelocities (void) const
	Whether or not the trajectory format supports velocities.
bool	hasForces (void) const
double	time (void) const
double	lambda (void) const
int	step (void) const
bool	parseFrame (void)
	Parse an actual frame.
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.
virtual double	velocityConversionFactor () const
	Conversion applied to velocities to get to \AA/ps.
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)

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 representing the GROMACS TRR trajectory files.

The TRR format can technically have differing numbers of atoms or even components (ie coords, velocities, forces) per frame. This is supported by LOOS, to an extent. If the components vary, then so long as there are coordinates, there should be no problem. If the number of atoms vary and you're using the updateGroupCoords() function, then care must be taken that the group matches the frame. Recall that the atomids are actually indices into the trajectory frame (ie atomid 1 takes its coords from the first trajectory coordinate, etc).

The TRR format can be written in either a single or double precision format. Internally, LOOS will read in either and translate it into whatever the default size is for LOOS (ie GCoord, which by default is a double). Metadata, such as lambda, or box sizes, are always upconverted to double by LOOS.

Since the TRR frame size is not fixed, the entire trajectory will be quickly scanned to build up an index of where the frames begin (see the loos::XTC class for more information).

Finally, note that GROMACS stores data in nm whereas LOOS uses angstroms, so coordinate/box data will be automatically scaled by LOOS.

Member Function Documentation

coords()

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

inlinevirtual

Returns the current frames coordinates as a vector of GCoords.

Some formats, notably DCDs, do not interleave their coordinates. This means that this could be a potentially expensive operation.

Implements loos::Trajectory.

description()

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

inlinevirtual

Return a string describing trajectory format.

Reimplemented from loos::Trajectory.

hasPeriodicBox()

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

inlinevirtual

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()

bool loos::TRR::hasVelocities ( void ) const

inlinevirtual

Whether or not the trajectory format supports velocities.

Reimplemented from loos::Trajectory.

natoms()

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

inlinevirtual

of atoms per frame

Implements loos::Trajectory.

nframes()

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

inlinevirtual

Number of frames in the trajectory.

Implements loos::Trajectory.

parseFrame()

bool loos::TRR::parseFrame ( void )

inlinevirtual

Parse an actual frame.

parseFrame() is expected to read in a frame through the Trajectory's StreamWrapper. It returns a bool indicating whether or not it was able to actually read a frame (i.e. false indicates EOF).

Implements loos::Trajectory.

periodicBox()

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

inlinevirtual

Returns the periodic box for the current frame/trajectory.

Implements loos::Trajectory.

timestep()

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

inlinevirtual

GROMACS trajectories do not define a timestep value as DCD does

Implements loos::Trajectory.

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

• src/trr.hpp
• src/trr.cpp