loos::TinkerArc Class Reference

Class for handling Tinker ARC files (concatenation of .xyz files) More...

#include <tinker_arc.hpp>

Inheritance diagram for loos::TinkerArc:

Collaboration diagram for loos::TinkerArc:

Public Member Functions
	TinkerArc (const std::string &s)
	TinkerArc (std::istream &is)
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 float	timestep (void) const
	Timestep per frame.
TinkerXYZ	currentFrame (void) const
	Returns the contained TinkerXYZ object.
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.
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 for handling Tinker ARC files (concatenation of .xyz files)

This class reads a concatenated .xyz tinker trajectory (i.e. an ARC file). In order to determine the number of frames present, the trajectory is scanned from beginning to end upon instantiation. A list of seek indices for each frame is also built.

The first frame is read in by init(), so there is no explicit readFrame() during initialization.

There seems to be an issue with some .ARC files where reading the end of the contained TinkerXYZ object does not put the input stream into an EOF state. So, we can't depend on checking eof() in parseFrame() to flag when we've iterated off the end. TinkerArc therefore keeps track of what index into the Trajectory it's at and uses that to check to see if it's at the end or not.

It is possible to get the contained TinkerXYZ object out of a TinkerArc, but with certain caveats. See CCPDB::currentFrame() for more details.

Member Function Documentation

coords()

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

virtual

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.

currentFrame()

TinkerXYZ loos::TinkerArc::currentFrame ( void ) const

inline

Returns the contained TinkerXYZ object.

See CCPDB::currentFrame() for some important notes about using this function.

description()

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

inlinevirtual

Return a string describing trajectory format.

Reimplemented from loos::Trajectory.

hasPeriodicBox()

virtual bool loos::TinkerArc::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::TinkerArc::natoms ( void ) const

inlinevirtual

of atoms per frame

Implements loos::Trajectory.

nframes()

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

inlinevirtual

Number of frames in the trajectory.

Implements loos::Trajectory.

parseFrame()

bool loos::TinkerArc::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::TinkerArc::periodicBox ( void ) const

inlinevirtual

Returns the periodic box for the current frame/trajectory.

Implements loos::Trajectory.

timestep()

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

inlinevirtual

Timestep per frame.

Implements loos::Trajectory.

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

• src/tinker_arc.hpp
• src/tinker_arc.cpp