Combine multiple trajectories (pTraj's) into one large virtual trajectory. More...

#include <MultiTraj.hpp>

Inheritance diagram for loos::MultiTrajectory:

Collaboration diagram for loos::MultiTrajectory:

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Public Types
typedef std::pair< uint, uint >	Location

Public Types inherited from loos::Trajectory
typedef boost::shared_ptr< std::istream >	pStream

Public Member Functions
	MultiTrajectory (const AtomicGroup &model)
	instantiate a new empty MultiTrajectory

	MultiTrajectory (const AtomicGroup &model, const uint skip, const uint stride)

	MultiTrajectory (const std::vector< std::string > &filenames, const AtomicGroup &model)
	Instantiate a new MultiTrajectory using the passed filenames.

	MultiTrajectory (const std::vector< std::string > &filenames, const AtomicGroup &model, const uint skip, const uint stride)

void	addTrajectory (const std::string &filename)
	Add a trajectory (by filename)

virtual std::string	description () const
	Return a string describing trajectory format.

virtual uint	natoms () const

virtual uint	nframes () const
	Total number of frames in composite trajectory.

uint	nframes (const uint i) const
	Number of frames in the ith trajectory.

uint	size () const
	Number of trajectories contained.

pTraj	operator[] (const uint i) const
	Access the individual trajectories.

virtual float	timestep () const
	Ignore timesteps (for now)

virtual bool	hasPeriodicBox () const
	Whether or not the current sub-trajectory has a periodic box.

virtual GCoord	periodicBox () const
	The periodic box of the current sub-trajectory.

virtual bool	hasVelocities () const
	Whether or not the current sub-trajectory has a periodic box.

virtual std::vector< GCoord >	coords () const
	Coordinates from the most recently read frame.

uint	currentTrajectoryIndex () const
	Index into the trajectory list for the trajectory currently used.

uint	currentFrameIndex () const
	Raw index into the current trajectory for the current frame (i.e. with skip & stride applied)

Location	frameIndexToLocation (const uint i)

bool	eof () const

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

Additional Inherited Members
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

Combine multiple trajectories (pTraj's) into one large virtual trajectory.

This class can be used just about anywhere a regular Trajectory/pTraj can be used. Note that the skip and stride settings are applied to each sub-trajectory (as opposed to the composite trajectory). They are also set ONLY at instantiation.

Member Function Documentation

◆ coords()

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

inlinevirtual

Coordinates from the most recently read frame.

Implements loos::Trajectory.

◆ description()

virtual std::string loos::MultiTrajectory::description ( ) const

inlinevirtual

Return a string describing trajectory format.

Reimplemented from loos::Trajectory.

◆ hasPeriodicBox()

virtual bool loos::MultiTrajectory::hasPeriodicBox ( void ) const

inlinevirtual

Whether or not the current sub-trajectory has a periodic box.

Implements loos::Trajectory.

◆ hasVelocities()

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

inlinevirtual

Whether or not the current sub-trajectory has a periodic box.

Reimplemented from loos::Trajectory.

◆ natoms()

virtual uint loos::MultiTrajectory::natoms ( ) const

inlinevirtual

of atoms per frame

Implements loos::Trajectory.

◆ nframes()

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

inlinevirtual

Total number of frames in composite trajectory.

Implements loos::Trajectory.

◆ periodicBox()

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

inlinevirtual

The periodic box of the current sub-trajectory.

Implements loos::Trajectory.

◆ timestep()

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

inlinevirtual

Ignore timesteps (for now)

Implements loos::Trajectory.

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

src/MultiTraj.hpp
src/MultiTraj.cpp

Public Types

Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ coords()

◆ description()

◆ hasPeriodicBox()

◆ hasVelocities()

◆ natoms()

of atoms per frame

◆ nframes()

◆ periodicBox()

◆ timestep()