loos::AmberTraj Class Reference

Class for reading amber coordinate trajectories. More...

#include <amber_traj.hpp>

Inheritance diagram for loos::AmberTraj:

Collaboration diagram for loos::AmberTraj:

Public Member Functions
	AmberTraj (const std::string &s, const int na)
	AmberTraj (std::istream &is, const int na)
std::string	description () const
	Return a string describing trajectory format.
virtual uint	nframes (void) const
	Number of frames in the trajectory.
virtual uint	natoms (void) const
virtual std::vector< GCoord >	coords (void) const
	Returns the current frames coordinates as a vector of GCoords.
virtual bool	hasPeriodicBox (void) const
virtual GCoord	periodicBox (void) const
	Returns the periodic box for the current frame/trajectory.
virtual double	velocityConversionFactor () const
	Conversion applied to velocities to get to \AA/ps.
virtual float	timestep (void) const
virtual 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 bool	hasVelocities () const
	Whether or not the trajectory format supports velocities.
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 for reading amber coordinate trajectories.

This class will read in the first frame of the trajectory upon instantiation. It will also scan the file to determine how many frames there are.

Since the Amber trajectory format does not store the # of atoms present, this must be passed to the AmberTraj constructor.

Note that the Amber timestep is (presumably) defined in the parmtop file, not in the trajectory file. So we return a null-value here...

Member Function Documentation

coords()

virtual std::vector< GCoord > loos::AmberTraj::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::AmberTraj::description ( ) const

inlinevirtual

Return a string describing trajectory format.

Reimplemented from loos::Trajectory.

hasPeriodicBox()

virtual bool loos::AmberTraj::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.

natoms()

virtual uint loos::AmberTraj::natoms ( void ) const

inlinevirtual

of atoms per frame

Implements loos::Trajectory.

nframes()

virtual uint loos::AmberTraj::nframes ( void ) const

inlinevirtual

Number of frames in the trajectory.

Implements loos::Trajectory.

parseFrame()

bool loos::AmberTraj::parseFrame ( void )

virtual

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()

virtual GCoord loos::AmberTraj::periodicBox ( void ) const

inlinevirtual

Returns the periodic box for the current frame/trajectory.

Implements loos::Trajectory.

timestep()

virtual float loos::AmberTraj::timestep ( void ) const

inlinevirtual

As stated above, Amber does not store the timestep in the trajectory, but in the parmtop instead. So we return a null-value here...

Implements loos::Trajectory.

velocityConversionFactor()

virtual double loos::AmberTraj::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/amber_traj.hpp
• src/amber_traj.cpp