loos::AmberNetcdf Class Reference

Class for reading Amber Trajectories in NetCDF format. More...

#include <amber_netcdf.hpp>

Inheritance diagram for loos::AmberNetcdf:

Collaboration diagram for loos::AmberNetcdf:

Public Member Functions
	AmberNetcdf (const std::string &s, const uint na)
std::string	description () const
	Return a string describing trajectory format.
uint	natoms () const
uint	nframes () const
	Number of frames in the trajectory.
float	timestep () const
	Timestep per frame.
bool	hasPeriodicBox () const
GCoord	periodicBox () const
	Returns the periodic box for the current frame/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.
std::vector< GCoord >	coords () const
	Returns the current frames coordinates as a vector of GCoords.
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.
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 reading Amber Trajectories in NetCDF format.

Member Function Documentation

coords()

std::vector< GCoord > loos::AmberNetcdf::coords ( ) const

inlinevirtual

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::AmberNetcdf::description ( ) const

inlinevirtual

Return a string describing trajectory format.

Reimplemented from loos::Trajectory.

hasPeriodicBox()

bool loos::AmberNetcdf::hasPeriodicBox ( ) 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.

hasVelocities()

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

inlinevirtual

Whether or not the trajectory format supports velocities.

Reimplemented from loos::Trajectory.

natoms()

uint loos::AmberNetcdf::natoms ( ) const

inlinevirtual

of atoms per frame

Implements loos::Trajectory.

nframes()

uint loos::AmberNetcdf::nframes ( ) const

inlinevirtual

Number of frames in the trajectory.

Implements loos::Trajectory.

periodicBox()

GCoord loos::AmberNetcdf::periodicBox ( ) const

inlinevirtual

Returns the periodic box for the current frame/trajectory.

Implements loos::Trajectory.

timestep()

float loos::AmberNetcdf::timestep ( ) const

inlinevirtual

Timestep per frame.

Implements loos::Trajectory.

velocityConversionFactor()

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

inlinevirtual

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

Reimplemented from loos::Trajectory.

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

• src/amber_netcdf.hpp
• src/amber_netcdf.cpp