Faunus::XTCReader Class Reference

Reads frames from an XTC file (GROMACS compressed trajectory file format). More...

#include <io.h>

Public Member Functions
	XTCReader (const std::string &filename)
int	getNumberOfCoordinates ()
	Returns number of coordinates (atoms) in each frame. More...
bool	read (TrajectoryFrame &frame)
	Reads the next frame in the trajectory from a file. More...
template<RequirePointIterator begin_iterator, typename end_iterator >
bool	read (int &step, float &time, Point &box, begin_iterator coordinates_begin, end_iterator coordinates_end)
	Reads the next frame in the trajectory. More...

Public Attributes
std::string	filename
	name of the trajectory file, mainly for error reporting

Protected Member Functions
bool	readFrame ()
	Actual wrapper around C function that reads the next frame into xtc_frame. More...

Detailed Description

Reads frames from an XTC file (GROMACS compressed trajectory file format).

It is a wrapper around C function calls.

Frames are stored into a TrajectoryFrame structure or as a list of positions in an output iterator. The class is responsible for I/O operations, not data conversion. For details about data conversion XTCTrajectoryFrame.

Constructor & Destructor Documentation

XTCReader()

Faunus::XTCReader::XTCReader ( const std::string &  filename )

explicit

Parameters

filename

a name of the XTC file to open

Member Function Documentation

getNumberOfCoordinates()

int Faunus::XTCReader::getNumberOfCoordinates

(

)

Returns number of coordinates (atoms) in each frame.

Immutable during object lifetime.

Returns

number of coordinates (atoms)

read() [1/2]

bool Faunus::XTCReader::read

(

TrajectoryFrame &

frame

)

Reads the next frame in the trajectory from a file.

Parameters

[out]

frame

target frame

Returns

true on success, false at the end of file

Exceptions

std::runtime_error

when other I/O error occures

read() [2/2]

template<RequirePointIterator begin_iterator, typename end_iterator >

bool Faunus::XTCReader::read ( int &  step, float &  time, Point &  box, begin_iterator  coordinates_begin, end_iterator  coordinates_end  )

inline

Reads the next frame in the trajectory.

Template Parameters

begin_iterator
end_iterator

Parameters

[out]	step	frame step
[out]	time	frame timestamp in picoseconds
[out]	box	box dimensions (xyz) in nanometers
[out]	coordinates_begin	output iterator to store coordinates
[out]	coordinates_end	output iterator's end

Returns

true on success, false at the end of file

Exceptions

std::runtime_error

when other I/O error occures

readFrame()

bool Faunus::XTCReader::readFrame ( )

protected

Actual wrapper around C function that reads the next frame into xtc_frame.

Returns

true on success, false at the end of file

Exceptions

std::runtime_error

when other I/O error occures

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

• src/io.h
• src/io.cpp