loos::PDBTraj Class Reference

Class for intepreting separate PDB files as a single trajectory. More...

#include <pdbtraj.hpp>

Inheritance diagram for loos::PDBTraj:

Collaboration diagram for loos::PDBTraj:

Public Member Functions
	PDBTraj (const std::string &s, uint st, uint en, uint str=1)
	PDBTraj (const char *p, uint st, uint en, uint str=1)
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 void	updateGroupCoords (AtomicGroup &g)
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.
std::string	currentName (void) const
	Returns the auto-generated name for the file containing the current frame.
PDB	currentFrame (void) const
	See CCPDB::currentFrame() for important notes.
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

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 intepreting separate PDB files as a single trajectory.

This class takes a set of PDB files following a specified naming pattern and accesses them as though they were a contiguous trajectory. You specify a template string (in boost::format format) and a start and end values along with an optional stride. Frame numbers are then mapped onto this range.

This first frame is read as part of initialization.

Access to the internal PDB object is permitted, however, see the CCPDB::currentFrame() for important information regarding its use.

Constructor & Destructor Documentation

PDBTraj()

loos::PDBTraj::PDBTraj ( const std::string & s, uint st, uint en, uint str = 1 )

inlineexplicit

Use the pattern s with starting index st, ending index en, and option stride str. As an example, suppose you have frames of the trajectory stored in PDB files named: -frame_000.pdb -frame_010.pdb -frame_020.pdb You can manipulate these as a trajectory using,

PDBTraj foo("frame_%03d.pdb", 0, 20, 10);

Member Function Documentation

coords()

std::vector< GCoord > loos::PDBTraj::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.

description()

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

inlinevirtual

Return a string describing trajectory format.

Reimplemented from loos::Trajectory.

hasPeriodicBox()

bool loos::PDBTraj::hasPeriodicBox ( void ) const

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.

Implements loos::Trajectory.

natoms()

uint loos::PDBTraj::natoms ( void ) const

virtual

of atoms per frame

Implements loos::Trajectory.

nframes()

uint loos::PDBTraj::nframes ( void ) const

virtual

Number of frames in the trajectory.

Implements loos::Trajectory.

parseFrame()

bool loos::PDBTraj::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()

GCoord loos::PDBTraj::periodicBox ( void ) const

virtual

Returns the periodic box for the current frame/trajectory.

Implements loos::Trajectory.

timestep()

float loos::PDBTraj::timestep ( void ) const

virtual

Timestep per frame.

Implements loos::Trajectory.

updateGroupCoords()

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

virtual

If the passed group to update is the same size as the trajectory frame, then the coordinates a copied straight out of the frame and into the group. If the sizes do not match, then the atomid's of the passed group are assumed to be indices (+1) into the frame.

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

• src/pdbtraj.hpp
• src/pdbtraj.cpp