loos::Trajectory Class Reference

Base-class for polymorphic trajectories. More...

#include <Trajectory.hpp>

Inheritance diagram for loos::Trajectory:

Collaboration diagram for loos::Trajectory:

Public Types
typedef boost::shared_ptr< std::istream >	pStream

Public Member Functions
	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	description () const
	Return a string describing trajectory format.
virtual std::string	filename () const
	Return the stored filename.
virtual uint	natoms (void) const =0
virtual float	timestep (void) const =0
	Timestep per frame.
virtual uint	nframes (void) const =0
	Number of frames in the 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.
bool	rewind (void)
	Rewinds the readFrame() iterator.
virtual bool	hasPeriodicBox (void) const =0
virtual GCoord	periodicBox (void) const =0
	Returns the periodic box for the current frame/trajectory.
virtual std::vector< GCoord >	coords (void) const =0
	Returns the current frames coordinates as a vector of GCoords.
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)
virtual bool	parseFrame (void)=0
	Parse an actual frame.
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

Protected Member Functions
void	setInputStream (const std::string &fname)
void	setInputStream (std::istream &fs)

Protected Attributes
pStream	ifs
bool	cached_first
std::string	_filename
uint	_current_frame

Detailed Description

Base-class for polymorphic trajectories.

This is the interface for trajectories in LOOS. It is expected that at least one frame of coordinates will be buffered internally at any given time.

Additionally, this class is not designed to provide output, only input...

+IMPORTANT NOTE+ The derived classes MUST read in and cache the first frame as part of their initialization. This prevents problems where updateGroupCoords() is called prior to the class reading any trajectory data (which can occur with some formats, such as DCD's, that only have to read a header to configure the internal data... However, just inserting a readFrame(0) in the constructor will leave the trajectory iterator in an incorrect state–the first call to readFrame() will return the 2nd frame, not the first, which is probably not the desired behavior. The derived class must also then set the cached_first flag to true after the readFrame(0). See the DCD class for an example of this.

Member Function Documentation

coords()

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

pure 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.

Implemented in loos::AmberNetcdf, loos::MultiTrajectory, loos::AmberRst, loos::AmberTraj, loos::CCPDB, loos::DCD, loos::MDTrajTraj, loos::PDBTraj, loos::TinkerArc, loos::TRR, and loos::XTC.

description()

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

inlinevirtual

Return a string describing trajectory format.

Reimplemented in loos::AmberNetcdf, loos::AmberRst, loos::AmberTraj, loos::CCPDB, loos::DCD, loos::MDTrajTraj, loos::MultiTrajectory, loos::PDBTraj, loos::TinkerArc, loos::TRR, and loos::XTC.

hasPeriodicBox()

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

pure 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.

Implemented in loos::AmberNetcdf, loos::MultiTrajectory, loos::AmberRst, loos::AmberTraj, loos::CCPDB, loos::DCD, loos::MDTrajTraj, loos::PDBTraj, loos::TinkerArc, loos::TRR, and loos::XTC.

hasVelocities()

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

inlinevirtual

Whether or not the trajectory format supports velocities.

Reimplemented in loos::AmberNetcdf, loos::DCD, loos::MultiTrajectory, and loos::TRR.

natoms()

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

pure virtual

of atoms per frame

Implemented in loos::AmberNetcdf, loos::MultiTrajectory, loos::AmberRst, loos::AmberTraj, loos::CCPDB, loos::DCD, loos::MDTrajTraj, loos::PDBTraj, loos::TinkerArc, loos::TRR, and loos::XTC.

nframes()

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

pure virtual

Number of frames in the trajectory.

Implemented in loos::AmberNetcdf, loos::MultiTrajectory, loos::AmberRst, loos::AmberTraj, loos::CCPDB, loos::DCD, loos::MDTrajTraj, loos::PDBTraj, loos::TinkerArc, loos::TRR, and loos::XTC.

parseFrame()

virtual bool loos::Trajectory::parseFrame ( void )

pure 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).

Implemented in loos::AmberRst, loos::AmberTraj, loos::CCPDB, loos::DCD, loos::MDTrajTraj, loos::PDBTraj, loos::TinkerArc, and loos::TRR.

periodicBox()

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

pure virtual

Returns the periodic box for the current frame/trajectory.

Implemented in loos::AmberNetcdf, loos::MultiTrajectory, loos::AmberRst, loos::AmberTraj, loos::CCPDB, loos::DCD, loos::MDTrajTraj, loos::PDBTraj, loos::TinkerArc, loos::TRR, and loos::XTC.

readFrame()

bool loos::Trajectory::readFrame ( const int i )

inline

Reads a specific frame in a trajectory.

Reading a specific frame also resets the readFrame() iterator version so it will continue where readFrame(i) left off...

seekFrame()

void loos::Trajectory::seekFrame ( const uint i )

inline

Seek to a specific frame, be it in the same contiguous file or in separate files.

seekNextFrame()

void loos::Trajectory::seekNextFrame ( void )

inline

Seek to the next frame in the sequence (used by readFrame() when operating as an iterator).

timestep()

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

pure virtual

Timestep per frame.

Implemented in loos::AmberNetcdf, loos::MultiTrajectory, loos::AmberRst, loos::AmberTraj, loos::CCPDB, loos::DCD, loos::MDTrajTraj, loos::PDBTraj, loos::TinkerArc, loos::TRR, and loos::XTC.

updateGroupCoords()

void loos::Trajectory::updateGroupCoords ( AtomicGroup & g )

inline

Update the coordinates in an AtomicGroup with the current frame.

The Atom::index() property is used as an index into the current frame for retrieving coordinates. The index property is typically set when a model is read in by the corresponding class (e.g. PDB, Amber, etc) and is determined by the ordering of the atoms in that file. This is not the same as an atomid. For example, the first atom in a structure could have an atomid of 1000, but its index would be 0.

updateGroupCoords() normally assumes that the passed AtomicGroup has valid indices. As a safety check, the createTrajectory() function will check that the AtomicGroup passed to it has indices. Only the first atom is tested, unless the DEBUG compile-flig is turned on, which will force updateGroupCoords() to validate the entire AtomicGroup every time, with correspondingly poorer performance.

Also note that the declaration of this function has changed in release 2.1.0. It is no longer virtual, using the NVI-idiom instead. Derived classes should override the updateGroupCoordsImpl() function.

velocities()

virtual std::vector< GCoord > loos::Trajectory::velocities ( void ) const

inlinevirtual

Returns the current frame's velocities as a vector of GCoords.

If the trajectory format supports velocities "natively", then those will be returned. If not, the velocities will be assumed to be stored in the coordinates. Those will be scaled by the velcotiyConversionFactor() and then returned.

velocityConversionFactor()

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

inlinevirtual

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

Reimplemented in loos::AmberNetcdf, loos::AmberTraj, and loos::DCD.

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

• src/Trajectory.hpp