PLMD::TrajectoryParser Class Reference

#include <TrajectoryParser.h>

Public Types
enum class	trajfmt {   molfile , xdr_xtc , xdr_trr , xyz ,   gro , dlp4 , error }

Public Member Functions
	TrajectoryParser ()
	~TrajectoryParser ()
std::optional< std::string >	init (std::string_view fmt, FILE *fileHandle)
std::optional< std::string >	init (std::string_view fmt, std::string_view fname, bool useMolfile=false, int command_line_natoms=-1)
int	nOfAtoms () const
	Return the number of atoms.
std::optional< std::string >	readAtoms (int stride, bool dont_read_pbc, bool debug_pd, int pd_start, int pd_nlocal, long long int &step, double *masses, double *charges, double *coordinates, double *cell)
std::optional< std::string >	readAtoms (int stride, bool dont_read_pbc, bool debug_pd, int pd_start, int pd_nlocal, long long int &step, float *masses, float *charges, float *coordinates, float *cell)
std::optional< std::string >	readFrame (int stride, bool dont_read_pbc, bool debug_pd, int pd_start, int pd_nlocal, long long int &step, double &timeStep, double *masses, double *charges, double *coordinates, double *cell)
std::optional< std::string >	readFrame (int stride, bool dont_read_pbc, bool debug_pd, int pd_start, int pd_nlocal, long long int &step, float &timeStep, float *masses, float *charges, float *coordinates, float *cell)
std::optional< std::string >	readHeader (long long int &step, double &timeStep)
std::optional< std::string >	readHeader (long long int &step, float &timeStep)
std::optional< std::string >	rewind ()
	Return the file pointer to the initial position (use at your own risk)

Static Public Member Functions
static trajfmt	FMTfromString (std::string_view fmt)
static std::vector< std::string >	getMolfilePluginsnames ()
static void	registerKeywords (Keywords &keys)
static std::string	toString (trajfmt fmt)
static std::vector< std::string >	trajectoryOptions ()

Private Attributes
std::unique_ptr< fileParser >	parser

Member Enumeration Documentation

trajfmt

enum class PLMD::TrajectoryParser::trajfmt

strong

Enumerator
molfile
xdr_xtc
xdr_trr
xyz
gro
dlp4
error

Constructor & Destructor Documentation

TrajectoryParser()

PLMD::TrajectoryParser::TrajectoryParser ( )

default

~TrajectoryParser()

PLMD::TrajectoryParser::~TrajectoryParser ( )

default

Member Function Documentation

FMTfromString()

TrajectoryParser::trajfmt PLMD::TrajectoryParser::FMTfromString ( std::string_view fmt )

static

getMolfilePluginsnames()

std::vector< std::string > PLMD::TrajectoryParser::getMolfilePluginsnames ( )

static

init() [1/2]

std::optional< std::string > PLMD::TrajectoryParser::init	(	std::string_view	fmt,
		FILE *	fileHandle )

init() [2/2]

std::optional< std::string > PLMD::TrajectoryParser::init	(	std::string_view	fmt,
		std::string_view	fname,
		bool	useMolfile = false,
		int	command_line_natoms = -1 )

nOfAtoms()

int PLMD::TrajectoryParser::nOfAtoms

(

)

const

Return the number of atoms.

readAtoms() [1/2]

std::optional< std::string > PLMD::TrajectoryParser::readAtoms	(	int	stride,
		bool	dont_read_pbc,
		bool	debug_pd,
		int	pd_start,
		int	pd_nlocal,
		long long int &	step,
		double *	masses,
		double *	charges,
		double *	coordinates,
		double *	cell )

readAtoms() [2/2]

std::optional< std::string > PLMD::TrajectoryParser::readAtoms	(	int	stride,
		bool	dont_read_pbc,
		bool	debug_pd,
		int	pd_start,
		int	pd_nlocal,
		long long int &	step,
		float *	masses,
		float *	charges,
		float *	coordinates,
		float *	cell )

readFrame() [1/2]

std::optional< std::string > PLMD::TrajectoryParser::readFrame	(	int	stride,
		bool	dont_read_pbc,
		bool	debug_pd,
		int	pd_start,
		int	pd_nlocal,
		long long int &	step,
		double &	timeStep,
		double *	masses,
		double *	charges,
		double *	coordinates,
		double *	cell )

readFrame() [2/2]

std::optional< std::string > PLMD::TrajectoryParser::readFrame	(	int	stride,
		bool	dont_read_pbc,
		bool	debug_pd,
		int	pd_start,
		int	pd_nlocal,
		long long int &	step,
		float &	timeStep,
		float *	masses,
		float *	charges,
		float *	coordinates,
		float *	cell )

readHeader() [1/2]

std::optional< std::string > PLMD::TrajectoryParser::readHeader	(	long long int &	step,
		double &	timeStep )

readHeader() [2/2]

std::optional< std::string > PLMD::TrajectoryParser::readHeader	(	long long int &	step,
		float &	timeStep )

registerKeywords()

void PLMD::TrajectoryParser::registerKeywords ( Keywords & keys )

static

rewind()

std::optional< std::string > PLMD::TrajectoryParser::rewind

(

)

Return the file pointer to the initial position (use at your own risk)

toString()

std::string PLMD::TrajectoryParser::toString ( trajfmt fmt )

static

trajectoryOptions()

std::vector< std::string > PLMD::TrajectoryParser::trajectoryOptions ( )

static

Member Data Documentation

parser

std::unique_ptr<fileParser> PLMD::TrajectoryParser::parser

private

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

• tools/TrajectoryParser.h
• tools/TrajectoryParser.cpp