loos::CCPDB Class Reference

Class for interpreting concatenated PDB files as a Trajectory. More...

#include <ccpdb.hpp>

Inheritance diagram for loos::CCPDB:

Collaboration diagram for loos::CCPDB:

Public Member Functions
	CCPDB (const std::string &s)
	CCPDB (const char *p)
	CCPDB (std::istream &is)
virtual 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
PDB	currentFrame (void) const
	Returns the current frame as a PDB 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 interpreting concatenated PDB files as a Trajectory.

This class reads a concatenated PDB Trajectory file as a LOOS Trajectory. Each frame of the trajectory must be separated by an "END" record. Since each frame is a fully-parsed PDB object, there is quite a bit of overhead involved in reading CCPDB trajectories. In addition, upon instantiation, the trajectory will be scanned for "END" records to build a list of seek indices for each frame.

It is possible to get the contained PDB object out of the CCPDB, but be careful of semantics that are slightly inconsistent with the rest of LOOS. See CCPDB::currentFrame() for more details.

Member Function Documentation

coords()

std::vector< GCoord > loos::CCPDB::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()

PDB loos::CCPDB::currentFrame ( void ) const

inline

Returns the current frame as a PDB object.

CCPDB actually stores a PDB object inside of it that represents the currently read frame. When you request that PDB, what you get is a shared copy with the internal one, that is, the contained Atom and PeriodicBox objects are shared. However, when you read in a new frame, the internal PDB is swapped out with a new one. So at this point, what you are left holding is actually a copy (equivalent to a deep copy) of the previously read frame.

In general, since currentFrame() is not part of the Trajectory interface, you should not use it unless you need it...

description()

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

inlinevirtual

Return a string describing trajectory format.

Reimplemented from loos::Trajectory.

hasPeriodicBox()

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

inlinevirtual

of atoms per frame

Implements loos::Trajectory.

nframes()

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

inlinevirtual

Number of frames in the trajectory.

Implements loos::Trajectory.

parseFrame()

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

inlinevirtual

Returns the periodic box for the current frame/trajectory.

Implements loos::Trajectory.

timestep()

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

inlinevirtual

The timestep is currently meaningless for CCPDB's, so we return a nominal 1e-3.

Implements loos::Trajectory.

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

• src/ccpdb.hpp
• src/ccpdb.cpp